| 4AIN_A |
| ID: | 1380272084 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 539 (494) | ||
| Sequences: | 1476 (1032.3) | ||
| Seq/Len: | 2.988 | ||
| 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: 2.988).
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 | 3.457 | 1.00 |
| 203_I | 440_S | 3.306 | 1.00 |
| 279_F | 413_M | 3.066 | 1.00 |
| 92_E | 350_R | 3.039 | 1.00 |
| 86_R | 93_A | 3.037 | 1.00 |
| 89_R | 92_E | 3.000 | 1.00 |
| 181_F | 198_I | 2.809 | 1.00 |
| 279_F | 283_V | 2.804 | 1.00 |
| 240_V | 464_L | 2.598 | 1.00 |
| 96_F | 259_G | 2.560 | 1.00 |
| 35_V | 39_G | 2.409 | 1.00 |
| 25_P | 200_I | 2.342 | 1.00 |
| 55_V | 487_T | 2.280 | 1.00 |
| 27_L | 454_A | 2.253 | 1.00 |
| 222_G | 238_T | 2.232 | 1.00 |
| 429_A | 459_T | 2.179 | 1.00 |
| 379_T | 407_L | 2.177 | 1.00 |
| 40_F | 43_S | 2.112 | 1.00 |
| 73_F | 497_M | 2.078 | 1.00 |
| 134_D | 137_N | 2.074 | 1.00 |
| 237_W | 241_G | 2.071 | 1.00 |
| 281_F | 375_I | 2.042 | 1.00 |
| 247_T | 460_A | 2.030 | 1.00 |
| 78_A | 359_L | 2.026 | 1.00 |
| 252_F | 256_S | 2.015 | 1.00 |
| 69_V | 494_I | 1.956 | 1.00 |
| 100_S | 267_N | 1.950 | 1.00 |
| 293_L | 374_S | 1.949 | 1.00 |
| 192_G | 195_G | 1.941 | 0.99 |
| 36_W | 43_S | 1.929 | 0.99 |
| 70_F | 493_V | 1.908 | 0.99 |
| 384_E | 389_S | 1.884 | 0.99 |
| 280_V | 407_L | 1.881 | 0.99 |
| 427_T | 431_S | 1.863 | 0.99 |
| 277_A | 375_I | 1.846 | 0.99 |
| 256_S | 264_Y | 1.833 | 0.99 |
| 336_S | 482_T | 1.830 | 0.99 |
| 66_F | 490_L | 1.802 | 0.99 |
| 281_F | 290_L | 1.786 | 0.99 |
| 178_S | 196_K | 1.782 | 0.99 |
| 66_F | 70_F | 1.777 | 0.99 |
| 92_E | 170_R | 1.767 | 0.99 |
| 80_S | 83_G | 1.759 | 0.99 |
| 491_F | 495_G | 1.759 | 0.99 |
| 146_M | 370_T | 1.757 | 0.99 |
| 78_A | 358_I | 1.754 | 0.99 |
| 354_I | 504_L | 1.751 | 0.99 |
| 123_L | 384_E | 1.746 | 0.99 |
| 253_S | 430_D | 1.742 | 0.99 |
| 292_L | 378_G | 1.741 | 0.99 |
| 222_G | 242_I | 1.724 | 0.99 |
| 67_G | 156_I | 1.713 | 0.98 |
| 244_S | 464_L | 1.700 | 0.98 |
| 273_A | 424_F | 1.697 | 0.98 |
| 235_S | 238_T | 1.692 | 0.98 |
| 185_I | 194_L | 1.677 | 0.98 |
| 75_V | 79_A | 1.662 | 0.98 |
| 73_F | 501_V | 1.662 | 0.98 |
| 433_S | 456_G | 1.658 | 0.98 |
| 466_L | 481_V | 1.651 | 0.98 |
| 187_E | 191_E | 1.643 | 0.98 |
| 232_E | 235_S | 1.630 | 0.98 |
| 153_P | 334_W | 1.627 | 0.98 |
| 126_Y | 385_Q | 1.624 | 0.98 |
| 150_T | 366_A | 1.617 | 0.98 |
| 422_G | 426_I | 1.607 | 0.97 |
| 429_A | 433_S | 1.602 | 0.97 |
| 173_R | 182_V | 1.593 | 0.97 |
| 222_G | 239_I | 1.580 | 0.97 |
| 255_I | 453_A | 1.579 | 0.97 |
| 97_R | 100_S | 1.576 | 0.97 |
| 157_Y | 334_W | 1.569 | 0.97 |
| 437_G | 451_V | 1.558 | 0.97 |
| 251_I | 255_I | 1.552 | 0.97 |
| 51_A | 484_V | 1.544 | 0.96 |
| 251_I | 456_G | 1.544 | 0.96 |
| 222_G | 233_D | 1.540 | 0.96 |
| 81_K | 84_T | 1.538 | 0.96 |
| 404_L | 417_A | 1.537 | 0.96 |
| 402_G | 405_H | 1.526 | 0.96 |
| 241_G | 245_V | 1.525 | 0.96 |
| 68_T | 309_G | 1.511 | 0.96 |
| 231_I | 238_T | 1.500 | 0.96 |
| 86_R | 91_D | 1.496 | 0.96 |
| 71_V | 75_V | 1.488 | 0.95 |
| 107_A | 423_T | 1.481 | 0.95 |
| 89_R | 170_R | 1.474 | 0.95 |
| 76_V | 501_V | 1.465 | 0.95 |
| 265_L | 430_D | 1.458 | 0.95 |
| 36_W | 44_F | 1.447 | 0.94 |
| 218_A | 242_I | 1.444 | 0.94 |
| 382_V | 386_N | 1.443 | 0.94 |
| 117_Y | 120_T | 1.432 | 0.94 |
| 271_V | 275_L | 1.431 | 0.94 |
| 33_T | 208_F | 1.426 | 0.94 |
| 160_V | 496_L | 1.414 | 0.93 |
| 110_M | 153_P | 1.413 | 0.93 |
| 95_E | 350_R | 1.406 | 0.93 |
| 51_A | 54_A | 1.405 | 0.93 |
| 216_L | 329_F | 1.399 | 0.93 |
| 89_R | 172_G | 1.377 | 0.92 |
| 232_E | 238_T | 1.376 | 0.92 |
| 103_S | 107_A | 1.370 | 0.92 |
| 163_A | 496_L | 1.364 | 0.92 |
| 294_P | 298_G | 1.362 | 0.92 |
| 85_I | 504_L | 1.355 | 0.91 |
| 247_T | 250_F | 1.353 | 0.91 |
| 98_T | 356_E | 1.351 | 0.91 |
| 178_S | 250_F | 1.343 | 0.91 |
| 201_L | 492_V | 1.342 | 0.91 |
| 96_F | 347_R | 1.338 | 0.91 |
| 457_V | 461_A | 1.331 | 0.90 |
| 293_L | 371_V | 1.330 | 0.90 |
| 404_L | 413_M | 1.324 | 0.90 |
| 77_I | 354_I | 1.321 | 0.90 |
| 194_L | 197_L | 1.305 | 0.89 |
| 412_I | 415_I | 1.297 | 0.89 |
| 296_S | 374_S | 1.295 | 0.89 |
| 186_G | 192_G | 1.293 | 0.89 |
| 83_G | 355_R | 1.293 | 0.89 |
| 226_S | 232_E | 1.290 | 0.88 |
| 79_A | 359_L | 1.290 | 0.88 |
| 143_S | 303_N | 1.290 | 0.88 |
| 38_I | 465_T | 1.289 | 0.88 |
| 180_A | 496_L | 1.284 | 0.88 |
| 201_L | 485_A | 1.281 | 0.88 |
| 63_F | 332_A | 1.272 | 0.88 |
| 90_I | 170_R | 1.272 | 0.88 |
| 193_W | 197_L | 1.268 | 0.87 |
| 82_F | 505_S | 1.263 | 0.87 |
| 182_V | 191_E | 1.251 | 0.86 |
| 302_S | 306_Q | 1.251 | 0.86 |
| 321_E | 325_S | 1.251 | 0.86 |
| 428_S | 431_S | 1.247 | 0.86 |
| 487_T | 491_F | 1.237 | 0.86 |
| 162_L | 354_I | 1.237 | 0.86 |
| 115_M | 421_L | 1.234 | 0.85 |
| 433_S | 459_T | 1.233 | 0.85 |
| 238_T | 241_G | 1.232 | 0.85 |
| 145_T | 373_F | 1.229 | 0.85 |
| 226_S | 233_D | 1.221 | 0.85 |
| 254_A | 456_G | 1.216 | 0.84 |
| 117_Y | 396_A | 1.216 | 0.84 |
| 224_G | 401_F | 1.212 | 0.84 |
| 504_L | 507_D | 1.208 | 0.84 |
| 86_R | 353_S | 1.203 | 0.83 |
| 167_S | 503_D | 1.197 | 0.83 |
| 254_A | 258_V | 1.196 | 0.83 |
| 250_F | 456_G | 1.195 | 0.83 |
| 185_I | 499_A | 1.193 | 0.83 |
| 79_A | 355_R | 1.189 | 0.82 |
| 184_L | 498_F | 1.183 | 0.82 |
| 225_L | 229_N | 1.178 | 0.82 |
| 409_G | 412_I | 1.174 | 0.81 |
| 173_R | 179_S | 1.170 | 0.81 |
| 183_P | 186_G | 1.166 | 0.81 |
| 178_S | 432_A | 1.165 | 0.81 |
| 182_V | 187_E | 1.161 | 0.80 |
| 222_G | 232_E | 1.160 | 0.80 |
| 268_A | 271_V | 1.159 | 0.80 |
| 54_A | 58_N | 1.155 | 0.80 |
| 44_F | 48_A | 1.149 | 0.79 |
| 374_S | 379_T | 1.145 | 0.79 |
| 260_K | 264_Y | 1.144 | 0.79 |
| 43_S | 47_F | 1.138 | 0.78 |
| 100_S | 263_Q | 1.137 | 0.78 |
| 281_F | 286_T | 1.136 | 0.78 |
| 68_T | 308_A | 1.136 | 0.78 |
| 70_F | 497_M | 1.132 | 0.78 |
| 285_P | 289_I | 1.131 | 0.78 |
| 46_N | 50_S | 1.131 | 0.78 |
| 62_A | 66_F | 1.130 | 0.78 |
| 69_V | 497_M | 1.129 | 0.78 |
| 80_S | 85_I | 1.129 | 0.78 |
| 407_L | 412_I | 1.127 | 0.77 |
| 476_S | 479_Q | 1.126 | 0.77 |
| 213_S | 217_G | 1.126 | 0.77 |
| 171_V | 503_D | 1.119 | 0.77 |
| 265_L | 423_T | 1.115 | 0.76 |
| 37_G | 44_F | 1.113 | 0.76 |
| 71_V | 155_A | 1.113 | 0.76 |
| 264_Y | 268_A | 1.113 | 0.76 |
| 175_Q | 178_S | 1.109 | 0.76 |
| 400_L | 417_A | 1.105 | 0.75 |
| 21_S | 196_K | 1.104 | 0.75 |
| 161_G | 166_Y | 1.103 | 0.75 |
| 185_I | 190_A | 1.101 | 0.75 |
| 61_W | 65_L | 1.099 | 0.75 |
| 86_R | 89_R | 1.098 | 0.75 |
| 96_F | 104_M | 1.098 | 0.75 |
| 251_I | 453_A | 1.093 | 0.74 |
| 47_F | 51_A | 1.085 | 0.74 |
| 99_V | 103_S | 1.085 | 0.74 |
| 36_W | 40_F | 1.084 | 0.73 |
| 173_R | 190_A | 1.083 | 0.73 |
| 120_T | 322_W | 1.081 | 0.73 |
| 53_S | 57_D | 1.081 | 0.73 |
| 293_L | 370_T | 1.080 | 0.73 |
| 60_G | 129_G | 1.080 | 0.73 |
| 410_G | 414_G | 1.073 | 0.72 |
| 158_A | 361_V | 1.073 | 0.72 |
| 343_M | 438_T | 1.071 | 0.72 |
| 21_S | 25_P | 1.071 | 0.72 |
| 167_S | 173_R | 1.064 | 0.71 |
| 138_V | 385_Q | 1.061 | 0.71 |
| 338_S | 493_V | 1.060 | 0.71 |
| 136_H | 140_V | 1.059 | 0.71 |
| 24_V | 28_V | 1.056 | 0.71 |
| 424_F | 428_S | 1.053 | 0.70 |
| 246_L | 422_G | 1.052 | 0.70 |
| 470_G | 474_A | 1.050 | 0.70 |
| 337_W | 428_S | 1.049 | 0.70 |
| 262_I | 431_S | 1.048 | 0.70 |
| 429_A | 456_G | 1.046 | 0.70 |
| 144_T | 307_M | 1.044 | 0.69 |
| 65_L | 294_P | 1.041 | 0.69 |
| 87_L | 354_I | 1.040 | 0.69 |
| 363_L | 367_G | 1.037 | 0.69 |
| 182_V | 190_A | 1.033 | 0.68 |
| 236_D | 468_L | 1.033 | 0.68 |
| 248_L | 252_F | 1.029 | 0.68 |
| 420_L | 423_T | 1.029 | 0.68 |
| 255_I | 449_K | 1.028 | 0.68 |
| 110_M | 114_L | 1.026 | 0.67 |
| 72_F | 76_V | 1.025 | 0.67 |
| 245_V | 249_A | 1.025 | 0.67 |
| 453_A | 457_V | 1.022 | 0.67 |
| 449_K | 452_T | 1.019 | 0.67 |
| 76_V | 79_A | 1.017 | 0.66 |
| 210_T | 262_I | 1.016 | 0.66 |
| 186_G | 195_G | 1.016 | 0.66 |
| 459_T | 463_G | 1.016 | 0.66 |
| 112_I | 217_G | 1.015 | 0.66 |
| 295_G | 313_M | 1.015 | 0.66 |
| 168_T | 175_Q | 1.015 | 0.66 |
| 236_D | 240_V | 1.014 | 0.66 |
| 327_T | 331_W | 1.011 | 0.66 |
| 345_L | 361_V | 1.008 | 0.65 |
| 95_E | 259_G | 1.007 | 0.65 |
| 222_G | 235_S | 1.005 | 0.65 |
| 119_T | 399_Q | 1.004 | 0.65 |
| 58_N | 287_V | 1.001 | 0.65 |
| 212_C | 479_Q | 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 | 0.065 | Contact Map |
| 2wswA | 1 | 0.9221 | 100 | 0.136 | Contact Map |
| 2xq2A | 1 | 0.7718 | 97.3 | 0.959 | Contact Map |
| 3dh4A | 4 | 0.7199 | 95 | 0.967 | Contact Map |
| 3l1lA | 1 | 0.679 | 94.1 | 0.969 | Contact Map |
| 2jlnA | 1 | 0.7161 | 90.6 | 0.972 | Contact Map |
| 3giaA | 1 | 0.6827 | 88.1 | 0.973 | Contact Map |
| 4djkA | 2 | 0.6716 | 81.8 | 0.976 | Contact Map |
| 4h33A | 1 | 0.1484 | 18.5 | 0.984 | Contact Map |
| 3effK | 4 | 0.2263 | 16.2 | 0.985 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)