| 1esw Amylomaltase from Thermus aquaticus |
| ID: | 1510614103 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 500 (483) | ||
| Sequences: | 2391 (1607.7) | ||
| Seq/Len: | 4.950 | ||
| Nf(neff/√len): | 73.2 |
HHblits Results: (2016_02)
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: 4.950).
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 |
| 101_Y | 181_E | 4.148 | 1.00 |
| 269_E | 323_K | 3.870 | 1.00 |
| 299_E | 348_E | 3.838 | 1.00 |
| 389_V | 439_G | 3.559 | 1.00 |
| 387_V | 444_A | 3.419 | 1.00 |
| 34_R | 202_E | 3.386 | 1.00 |
| 33_L | 203_A | 3.297 | 1.00 |
| 149_G | 181_E | 3.178 | 1.00 |
| 131_R | 186_A | 3.007 | 1.00 |
| 211_I | 338_L | 2.980 | 1.00 |
| 14_T | 71_L | 2.975 | 1.00 |
| 37_K | 206_L | 2.877 | 1.00 |
| 454_V | 490_L | 2.853 | 1.00 |
| 67_G | 192_F | 2.716 | 1.00 |
| 254_T | 312_V | 2.710 | 1.00 |
| 391_T | 450_P | 2.633 | 1.00 |
| 200_K | 204_E | 2.622 | 1.00 |
| 231_W | 268_L | 2.601 | 1.00 |
| 127_F | 186_A | 2.600 | 1.00 |
| 139_E | 186_A | 2.542 | 1.00 |
| 41_G | 494_A | 2.465 | 1.00 |
| 7_F | 494_A | 2.400 | 1.00 |
| 242_V | 303_E | 2.366 | 1.00 |
| 112_F | 183_A | 2.361 | 1.00 |
| 12_H | 463_M | 2.352 | 1.00 |
| 163_L | 174_A | 2.309 | 1.00 |
| 268_L | 271_E | 2.255 | 1.00 |
| 273_F | 319_A | 2.246 | 1.00 |
| 142_A | 186_A | 2.236 | 1.00 |
| 148_K | 221_D | 2.212 | 1.00 |
| 432_P | 456_A | 2.210 | 1.00 |
| 440_M | 449_Y | 2.207 | 1.00 |
| 233_H | 303_E | 2.198 | 1.00 |
| 43_Y | 211_I | 2.175 | 1.00 |
| 173_E | 177_A | 2.172 | 1.00 |
| 201_A | 205_A | 2.149 | 1.00 |
| 398_T | 401_G | 2.119 | 1.00 |
| 433_W | 489_R | 2.098 | 1.00 |
| 267_V | 270_R | 2.044 | 1.00 |
| 267_V | 271_E | 1.998 | 1.00 |
| 14_T | 463_M | 1.966 | 1.00 |
| 72_I | 191_L | 1.964 | 1.00 |
| 416_R | 492_A | 1.958 | 1.00 |
| 303_E | 317_V | 1.951 | 1.00 |
| 127_F | 183_A | 1.948 | 1.00 |
| 441_K | 497_T | 1.939 | 1.00 |
| 257_R | 304_I | 1.919 | 1.00 |
| 46_V | 210_I | 1.894 | 1.00 |
| 269_E | 273_F | 1.892 | 1.00 |
| 166_R | 171_L | 1.851 | 1.00 |
| 161_L | 164_R | 1.845 | 1.00 |
| 112_F | 187_F | 1.842 | 1.00 |
| 97_Y | 184_F | 1.832 | 1.00 |
| 351_A | 355_R | 1.807 | 1.00 |
| 264_R | 267_V | 1.803 | 1.00 |
| 127_F | 131_R | 1.790 | 1.00 |
| 271_E | 274_S | 1.788 | 1.00 |
| 24_V | 96_D | 1.788 | 1.00 |
| 7_F | 41_G | 1.780 | 1.00 |
| 451_V | 477_L | 1.779 | 1.00 |
| 231_W | 271_E | 1.775 | 1.00 |
| 299_E | 318_K | 1.766 | 1.00 |
| 40_G | 491_R | 1.765 | 1.00 |
| 298_F | 325_F | 1.754 | 1.00 |
| 43_Y | 446_L | 1.723 | 1.00 |
| 36_L | 41_G | 1.695 | 0.99 |
| 257_R | 307_S | 1.693 | 0.99 |
| 26_G | 73_D | 1.689 | 0.99 |
| 131_R | 139_E | 1.686 | 0.99 |
| 323_K | 326_Q | 1.685 | 0.99 |
| 278_R | 281_E | 1.669 | 0.99 |
| 225_V | 234_L | 1.668 | 0.99 |
| 24_V | 73_D | 1.665 | 0.99 |
| 193_F | 286_L | 1.654 | 0.99 |
| 72_I | 192_F | 1.654 | 0.99 |
| 40_G | 500_L | 1.648 | 0.99 |
| 440_M | 494_A | 1.639 | 0.99 |
| 225_V | 232_F | 1.613 | 0.99 |
| 274_S | 278_R | 1.610 | 0.99 |
| 193_F | 282_K | 1.591 | 0.99 |
| 381_Y | 389_V | 1.589 | 0.99 |
| 273_F | 323_K | 1.588 | 0.99 |
| 165_K | 229_P | 1.570 | 0.99 |
| 143_L | 175_K | 1.554 | 0.99 |
| 284_L | 335_V | 1.546 | 0.99 |
| 149_G | 185_H | 1.545 | 0.99 |
| 33_L | 206_L | 1.526 | 0.99 |
| 300_A | 348_E | 1.520 | 0.99 |
| 439_G | 447_A | 1.515 | 0.99 |
| 322_E | 355_R | 1.509 | 0.99 |
| 167_E | 170_A | 1.507 | 0.99 |
| 191_L | 194_R | 1.474 | 0.98 |
| 33_L | 199_L | 1.467 | 0.98 |
| 9_L | 451_V | 1.467 | 0.98 |
| 33_L | 202_E | 1.456 | 0.98 |
| 326_Q | 356_F | 1.447 | 0.98 |
| 147_L | 163_L | 1.446 | 0.98 |
| 116_K | 180_E | 1.444 | 0.98 |
| 400_L | 404_R | 1.441 | 0.98 |
| 89_G | 474_A | 1.433 | 0.98 |
| 230_E | 267_V | 1.426 | 0.98 |
| 88_P | 478_L | 1.424 | 0.98 |
| 147_L | 174_A | 1.423 | 0.98 |
| 436_M | 449_Y | 1.417 | 0.98 |
| 76_P | 198_A | 1.413 | 0.98 |
| 392_G | 396_N | 1.404 | 0.97 |
| 9_L | 36_L | 1.402 | 0.97 |
| 131_R | 183_A | 1.402 | 0.97 |
| 367_A | 376_F | 1.400 | 0.97 |
| 491_R | 500_L | 1.400 | 0.97 |
| 100_L | 188_T | 1.394 | 0.97 |
| 130_F | 138_L | 1.394 | 0.97 |
| 203_A | 206_L | 1.393 | 0.97 |
| 202_E | 206_L | 1.391 | 0.97 |
| 282_K | 285_E | 1.386 | 0.97 |
| 133_R | 285_E | 1.384 | 0.97 |
| 136_W | 140_D | 1.372 | 0.97 |
| 437_H | 496_A | 1.364 | 0.97 |
| 182_V | 186_A | 1.359 | 0.97 |
| 174_A | 177_A | 1.357 | 0.97 |
| 30_R | 199_L | 1.357 | 0.97 |
| 362_K | 387_V | 1.351 | 0.96 |
| 281_E | 331_V | 1.350 | 0.96 |
| 491_R | 495_E | 1.348 | 0.96 |
| 43_Y | 289_L | 1.339 | 0.96 |
| 322_E | 326_Q | 1.339 | 0.96 |
| 142_A | 182_V | 1.333 | 0.96 |
| 73_D | 76_P | 1.331 | 0.96 |
| 18_G | 28_E | 1.327 | 0.96 |
| 233_H | 264_R | 1.323 | 0.96 |
| 9_L | 454_V | 1.321 | 0.96 |
| 35_F | 39_A | 1.321 | 0.96 |
| 271_E | 275_F | 1.314 | 0.96 |
| 184_F | 188_T | 1.313 | 0.96 |
| 72_I | 188_T | 1.304 | 0.95 |
| 397_D | 401_G | 1.299 | 0.95 |
| 403_Y | 431_V | 1.299 | 0.95 |
| 112_F | 116_K | 1.296 | 0.95 |
| 290_V | 337_V | 1.295 | 0.95 |
| 230_E | 271_E | 1.293 | 0.95 |
| 379_H | 417_Y | 1.291 | 0.95 |
| 28_E | 31_D | 1.288 | 0.95 |
| 365_Q | 399_T | 1.286 | 0.95 |
| 233_H | 262_L | 1.283 | 0.95 |
| 283_A | 290_V | 1.278 | 0.95 |
| 277_I | 331_V | 1.277 | 0.95 |
| 284_L | 290_V | 1.277 | 0.95 |
| 129_A | 133_R | 1.262 | 0.94 |
| 127_F | 138_L | 1.262 | 0.94 |
| 155_P | 158_R | 1.254 | 0.94 |
| 79_E | 123_E | 1.253 | 0.94 |
| 187_F | 191_L | 1.242 | 0.94 |
| 350_E | 354_D | 1.241 | 0.94 |
| 217_F | 262_L | 1.241 | 0.94 |
| 70_Y | 92_Q | 1.228 | 0.93 |
| 242_V | 317_V | 1.226 | 0.93 |
| 362_K | 376_F | 1.226 | 0.93 |
| 29_A | 199_L | 1.226 | 0.93 |
| 400_L | 456_A | 1.225 | 0.93 |
| 34_R | 206_L | 1.221 | 0.93 |
| 7_F | 440_M | 1.219 | 0.93 |
| 30_R | 202_E | 1.214 | 0.93 |
| 350_E | 353_R | 1.213 | 0.93 |
| 361_M | 390_Y | 1.210 | 0.92 |
| 145_M | 185_H | 1.210 | 0.92 |
| 146_A | 182_V | 1.209 | 0.92 |
| 321_G | 352_L | 1.208 | 0.92 |
| 204_E | 288_H | 1.207 | 0.92 |
| 389_V | 444_A | 1.202 | 0.92 |
| 492_A | 496_A | 1.200 | 0.92 |
| 70_Y | 93_G | 1.200 | 0.92 |
| 30_R | 198_A | 1.198 | 0.92 |
| 299_E | 346_T | 1.196 | 0.92 |
| 300_A | 344_V | 1.195 | 0.92 |
| 40_G | 495_E | 1.190 | 0.92 |
| 171_L | 175_K | 1.189 | 0.92 |
| 300_A | 346_T | 1.184 | 0.91 |
| 112_F | 184_F | 1.180 | 0.91 |
| 10_L | 448_V | 1.178 | 0.91 |
| 216_I | 297_G | 1.178 | 0.91 |
| 113_R | 180_E | 1.177 | 0.91 |
| 6_A | 446_L | 1.175 | 0.91 |
| 6_A | 43_Y | 1.174 | 0.91 |
| 277_I | 281_E | 1.169 | 0.91 |
| 97_Y | 101_Y | 1.167 | 0.91 |
| 15_S | 463_M | 1.163 | 0.90 |
| 183_A | 186_A | 1.162 | 0.90 |
| 244_A | 260_N | 1.159 | 0.90 |
| 468_R | 472_N | 1.151 | 0.90 |
| 115_F | 127_F | 1.150 | 0.90 |
| 136_W | 278_R | 1.148 | 0.90 |
| 320_P | 324_L | 1.148 | 0.90 |
| 254_T | 310_T | 1.140 | 0.89 |
| 166_R | 229_P | 1.126 | 0.88 |
| 233_H | 242_V | 1.116 | 0.88 |
| 27_R | 31_D | 1.111 | 0.88 |
| 22_V | 92_Q | 1.109 | 0.87 |
| 437_H | 497_T | 1.108 | 0.87 |
| 101_Y | 149_G | 1.106 | 0.87 |
| 139_E | 175_K | 1.104 | 0.87 |
| 418_L | 438_L | 1.104 | 0.87 |
| 440_M | 447_A | 1.104 | 0.87 |
| 471_G | 474_A | 1.101 | 0.87 |
| 370_D | 373_E | 1.101 | 0.87 |
| 310_T | 313_E | 1.099 | 0.87 |
| 322_E | 356_F | 1.095 | 0.86 |
| 25_L | 192_F | 1.094 | 0.86 |
| 438_L | 442_S | 1.092 | 0.86 |
| 20_Y | 74_L | 1.090 | 0.86 |
| 101_Y | 184_F | 1.089 | 0.86 |
| 146_A | 185_H | 1.085 | 0.86 |
| 130_F | 193_F | 1.083 | 0.86 |
| 404_R | 458_G | 1.077 | 0.85 |
| 172_R | 175_K | 1.076 | 0.85 |
| 272_G | 277_I | 1.072 | 0.85 |
| 399_T | 435_L | 1.072 | 0.85 |
| 98_G | 102_A | 1.071 | 0.85 |
| 146_A | 174_A | 1.062 | 0.84 |
| 345_I | 350_E | 1.062 | 0.84 |
| 400_L | 432_P | 1.050 | 0.83 |
| 301_Y | 319_A | 1.042 | 0.83 |
| 492_A | 495_E | 1.038 | 0.82 |
| 347_P | 350_E | 1.038 | 0.82 |
| 127_F | 190_W | 1.036 | 0.82 |
| 274_S | 331_V | 1.034 | 0.82 |
| 211_I | 289_L | 1.032 | 0.82 |
| 141_Y | 223_A | 1.025 | 0.81 |
| 56_D | 90_F | 1.021 | 0.81 |
| 43_Y | 448_V | 1.020 | 0.81 |
| 126_A | 194_R | 1.020 | 0.81 |
| 22_V | 96_D | 1.016 | 0.80 |
| 12_H | 71_L | 1.014 | 0.80 |
| 229_P | 238_G | 1.013 | 0.80 |
| 389_V | 447_A | 1.012 | 0.80 |
| 303_E | 315_R | 1.010 | 0.80 |
| 127_F | 130_F | 1.007 | 0.80 |
| 174_A | 178_L | 1.001 | 0.79 |
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 | |
| 1eswA | 1 | 0.98 | 100 | 0.025 | Contact Map |
| 1tz7A | 2 | 0.952 | 100 | 0.041 | Contact Map |
| 1x1nA | 1 | 0.968 | 100 | 0.047 | Contact Map |
| 4s3qA | 3 | 0 | 100 | 0.074 | Contact Map |
| 1ht6A | 1 | 0.636 | 98.5 | 0.938 | Contact Map |
| 4bzyA | 3 | 0.69 | 98.5 | 0.938 | Contact Map |
| 3amlA | 1 | 0.708 | 98.4 | 0.939 | Contact Map |
| 3zssA | 4 | 0.67 | 98.3 | 0.94 | Contact Map |
| 4aefA | 2 | 0.63 | 98.3 | 0.941 | Contact Map |
| 4gklA | 2 | 0.61 | 98.2 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)