| ytyt |
| ID: | 1386194907 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 583 (551) | ||
| Sequences: | 1840 (1211.9) | ||
| Seq/Len: | 3.339 | ||
| Nf(neff/√len): | 51.6 |
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: 3.339).
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 |
| 126_C | 131_C | 3.250 | 1.00 |
| 333_P | 459_G | 2.916 | 1.00 |
| 420_S | 532_G | 2.848 | 1.00 |
| 93_I | 98_T | 2.569 | 1.00 |
| 38_E | 41_E | 2.402 | 1.00 |
| 38_E | 42_R | 2.307 | 1.00 |
| 112_L | 145_S | 2.172 | 1.00 |
| 102_S | 155_G | 2.137 | 1.00 |
| 380_M | 384_S | 2.111 | 1.00 |
| 204_I | 216_I | 2.107 | 1.00 |
| 41_E | 157_K | 2.035 | 1.00 |
| 366_L | 446_I | 2.001 | 1.00 |
| 348_G | 446_I | 1.999 | 1.00 |
| 38_E | 157_K | 1.998 | 1.00 |
| 88_I | 93_I | 1.951 | 1.00 |
| 526_R | 529_Y | 1.939 | 1.00 |
| 417_A | 535_V | 1.938 | 1.00 |
| 334_S | 464_A | 1.927 | 1.00 |
| 14_D | 20_V | 1.909 | 1.00 |
| 109_G | 152_G | 1.904 | 1.00 |
| 166_D | 472_Y | 1.885 | 0.99 |
| 14_D | 18_R | 1.870 | 0.99 |
| 539_I | 543_G | 1.861 | 0.99 |
| 407_V | 462_F | 1.852 | 0.99 |
| 140_T | 144_I | 1.786 | 0.99 |
| 388_F | 392_K | 1.758 | 0.99 |
| 104_L | 108_L | 1.749 | 0.99 |
| 14_D | 19_P | 1.742 | 0.99 |
| 186_W | 190_S | 1.733 | 0.99 |
| 14_D | 17_G | 1.722 | 0.99 |
| 109_G | 149_I | 1.717 | 0.99 |
| 376_L | 380_M | 1.717 | 0.99 |
| 114_T | 218_T | 1.693 | 0.99 |
| 262_L | 301_I | 1.690 | 0.99 |
| 253_P | 257_F | 1.681 | 0.99 |
| 353_R | 360_Q | 1.674 | 0.99 |
| 232_T | 237_H | 1.653 | 0.98 |
| 352_D | 443_P | 1.652 | 0.98 |
| 195_L | 375_L | 1.632 | 0.98 |
| 519_G | 525_S | 1.632 | 0.98 |
| 282_N | 285_H | 1.623 | 0.98 |
| 425_K | 428_R | 1.606 | 0.98 |
| 81_T | 84_A | 1.596 | 0.98 |
| 38_E | 156_T | 1.592 | 0.98 |
| 231_G | 235_Y | 1.589 | 0.98 |
| 467_L | 487_F | 1.584 | 0.98 |
| 414_V | 418_I | 1.570 | 0.98 |
| 164_G | 182_F | 1.568 | 0.97 |
| 107_V | 222_L | 1.538 | 0.97 |
| 25_T | 28_W | 1.537 | 0.97 |
| 546_V | 549_A | 1.536 | 0.97 |
| 544_L | 548_A | 1.527 | 0.97 |
| 423_E | 426_R | 1.527 | 0.97 |
| 71_V | 342_T | 1.512 | 0.97 |
| 93_I | 101_A | 1.508 | 0.97 |
| 187_M | 460_D | 1.502 | 0.97 |
| 86_A | 481_S | 1.500 | 0.96 |
| 113_L | 145_S | 1.499 | 0.96 |
| 464_A | 468_L | 1.499 | 0.96 |
| 289_H | 297_D | 1.495 | 0.96 |
| 84_A | 88_I | 1.474 | 0.96 |
| 410_A | 414_V | 1.462 | 0.96 |
| 172_S | 175_E | 1.454 | 0.96 |
| 13_V | 17_G | 1.453 | 0.96 |
| 8_T | 11_G | 1.446 | 0.95 |
| 384_S | 388_F | 1.440 | 0.95 |
| 82_P | 89_A | 1.438 | 0.95 |
| 87_Y | 92_Y | 1.425 | 0.95 |
| 374_M | 460_D | 1.424 | 0.95 |
| 187_M | 374_M | 1.422 | 0.95 |
| 542_M | 546_V | 1.421 | 0.95 |
| 75_S | 78_V | 1.413 | 0.95 |
| 400_T | 403_Q | 1.409 | 0.94 |
| 402_L | 549_A | 1.404 | 0.94 |
| 64_T | 346_K | 1.400 | 0.94 |
| 421_A | 425_K | 1.397 | 0.94 |
| 381_Y | 385_F | 1.396 | 0.94 |
| 44_A | 110_M | 1.390 | 0.94 |
| 351_L | 449_L | 1.390 | 0.94 |
| 333_P | 463_N | 1.383 | 0.94 |
| 373_S | 457_G | 1.383 | 0.94 |
| 347_Q | 449_L | 1.381 | 0.94 |
| 531_Y | 534_L | 1.368 | 0.93 |
| 255_A | 259_N | 1.367 | 0.93 |
| 11_G | 14_D | 1.359 | 0.93 |
| 283_G | 286_Q | 1.354 | 0.93 |
| 14_D | 25_T | 1.350 | 0.93 |
| 95_R | 166_D | 1.345 | 0.93 |
| 429_V | 442_V | 1.340 | 0.92 |
| 42_R | 45_F | 1.339 | 0.92 |
| 418_I | 455_L | 1.338 | 0.92 |
| 100_T | 229_Y | 1.338 | 0.92 |
| 42_R | 157_K | 1.335 | 0.92 |
| 13_V | 20_V | 1.325 | 0.92 |
| 169_D | 236_R | 1.325 | 0.92 |
| 15_L | 21_L | 1.324 | 0.92 |
| 87_Y | 246_A | 1.319 | 0.92 |
| 55_Y | 116_A | 1.318 | 0.92 |
| 419_A | 452_Q | 1.315 | 0.91 |
| 111_I | 115_M | 1.314 | 0.91 |
| 156_T | 160_I | 1.314 | 0.91 |
| 42_R | 46_Y | 1.311 | 0.91 |
| 444_M | 448_W | 1.310 | 0.91 |
| 416_I | 535_V | 1.310 | 0.91 |
| 377_S | 458_I | 1.307 | 0.91 |
| 38_E | 186_W | 1.299 | 0.91 |
| 296_L | 299_A | 1.297 | 0.91 |
| 251_Q | 313_K | 1.297 | 0.91 |
| 315_E | 318_K | 1.297 | 0.91 |
| 40_F | 160_I | 1.290 | 0.90 |
| 393_T | 398_G | 1.287 | 0.90 |
| 15_L | 20_V | 1.285 | 0.90 |
| 297_D | 300_A | 1.284 | 0.90 |
| 309_C | 313_K | 1.284 | 0.90 |
| 243_D | 246_A | 1.282 | 0.90 |
| 14_D | 22_A | 1.279 | 0.90 |
| 41_E | 221_L | 1.272 | 0.89 |
| 13_V | 16_Q | 1.269 | 0.89 |
| 256_A | 260_R | 1.258 | 0.89 |
| 45_F | 75_S | 1.249 | 0.88 |
| 108_L | 112_L | 1.247 | 0.88 |
| 11_G | 20_V | 1.243 | 0.88 |
| 78_V | 150_A | 1.243 | 0.88 |
| 168_F | 182_F | 1.242 | 0.88 |
| 197_A | 336_L | 1.240 | 0.88 |
| 17_G | 20_V | 1.240 | 0.88 |
| 86_A | 485_T | 1.236 | 0.88 |
| 459_G | 480_Q | 1.234 | 0.88 |
| 11_G | 22_A | 1.232 | 0.87 |
| 81_T | 150_A | 1.231 | 0.87 |
| 191_F | 370_V | 1.230 | 0.87 |
| 437_S | 524_D | 1.229 | 0.87 |
| 417_A | 532_G | 1.227 | 0.87 |
| 240_I | 243_D | 1.225 | 0.87 |
| 204_I | 208_L | 1.217 | 0.87 |
| 295_F | 299_A | 1.213 | 0.86 |
| 219_V | 223_V | 1.205 | 0.86 |
| 424_V | 428_R | 1.203 | 0.86 |
| 540_V | 543_G | 1.200 | 0.85 |
| 389_M | 394_G | 1.199 | 0.85 |
| 252_V | 314_V | 1.197 | 0.85 |
| 186_W | 468_L | 1.197 | 0.85 |
| 20_V | 25_T | 1.194 | 0.85 |
| 349_T | 363_A | 1.191 | 0.85 |
| 103_S | 217_P | 1.189 | 0.85 |
| 327_W | 471_F | 1.188 | 0.85 |
| 165_A | 472_Y | 1.188 | 0.85 |
| 159_N | 217_P | 1.185 | 0.84 |
| 306_R | 309_C | 1.181 | 0.84 |
| 77_A | 496_F | 1.181 | 0.84 |
| 404_R | 457_G | 1.176 | 0.84 |
| 161_S | 468_L | 1.173 | 0.84 |
| 78_V | 81_T | 1.173 | 0.84 |
| 27_R | 30_A | 1.170 | 0.83 |
| 38_E | 47_G | 1.168 | 0.83 |
| 42_R | 47_G | 1.166 | 0.83 |
| 96_F | 232_T | 1.165 | 0.83 |
| 10_D | 13_V | 1.165 | 0.83 |
| 203_Y | 208_L | 1.165 | 0.83 |
| 83_I | 87_Y | 1.164 | 0.83 |
| 9_Q | 12_T | 1.162 | 0.83 |
| 53_V | 324_I | 1.161 | 0.83 |
| 333_P | 374_M | 1.159 | 0.83 |
| 385_F | 389_M | 1.157 | 0.83 |
| 252_V | 256_A | 1.157 | 0.83 |
| 107_V | 225_L | 1.155 | 0.82 |
| 79_W | 157_K | 1.151 | 0.82 |
| 8_T | 12_T | 1.148 | 0.82 |
| 468_L | 487_F | 1.147 | 0.82 |
| 166_D | 480_Q | 1.147 | 0.82 |
| 284_K | 303_T | 1.144 | 0.82 |
| 417_A | 421_A | 1.143 | 0.81 |
| 347_Q | 351_L | 1.141 | 0.81 |
| 51_N | 56_L | 1.141 | 0.81 |
| 39_A | 189_S | 1.137 | 0.81 |
| 137_L | 141_F | 1.133 | 0.81 |
| 72_N | 499_S | 1.132 | 0.81 |
| 145_S | 335_T | 1.129 | 0.80 |
| 337_W | 340_V | 1.129 | 0.80 |
| 52_L | 56_L | 1.129 | 0.80 |
| 85_G | 154_G | 1.128 | 0.80 |
| 57_T | 346_K | 1.127 | 0.80 |
| 11_G | 19_P | 1.125 | 0.80 |
| 424_V | 528_D | 1.124 | 0.80 |
| 418_I | 452_Q | 1.115 | 0.79 |
| 272_Y | 289_H | 1.115 | 0.79 |
| 206_E | 363_A | 1.113 | 0.79 |
| 422_V | 444_M | 1.111 | 0.79 |
| 153_A | 157_K | 1.111 | 0.79 |
| 69_R | 73_N | 1.111 | 0.79 |
| 40_F | 44_A | 1.109 | 0.79 |
| 131_C | 134_A | 1.108 | 0.79 |
| 13_V | 18_R | 1.106 | 0.78 |
| 44_A | 48_I | 1.102 | 0.78 |
| 247_K | 251_Q | 1.101 | 0.78 |
| 157_K | 190_S | 1.100 | 0.78 |
| 8_T | 19_P | 1.098 | 0.78 |
| 164_G | 167_Q | 1.098 | 0.78 |
| 259_N | 308_P | 1.095 | 0.77 |
| 22_A | 172_S | 1.093 | 0.77 |
| 230_I | 548_A | 1.092 | 0.77 |
| 218_T | 222_L | 1.092 | 0.77 |
| 53_V | 57_T | 1.092 | 0.77 |
| 54_N | 363_A | 1.092 | 0.77 |
| 174_E | 391_K | 1.091 | 0.77 |
| 161_S | 190_S | 1.091 | 0.77 |
| 362_P | 365_S | 1.088 | 0.77 |
| 13_V | 22_A | 1.087 | 0.77 |
| 210_W | 214_Y | 1.086 | 0.77 |
| 38_E | 374_M | 1.086 | 0.77 |
| 114_T | 215_G | 1.085 | 0.77 |
| 230_I | 233_P | 1.085 | 0.77 |
| 18_R | 23_S | 1.083 | 0.76 |
| 464_A | 467_L | 1.083 | 0.76 |
| 12_T | 21_L | 1.082 | 0.76 |
| 45_F | 157_K | 1.077 | 0.76 |
| 209_G | 212_L | 1.075 | 0.76 |
| 30_A | 33_F | 1.074 | 0.76 |
| 38_E | 46_Y | 1.073 | 0.75 |
| 353_R | 363_A | 1.073 | 0.75 |
| 13_V | 19_P | 1.071 | 0.75 |
| 200_G | 384_S | 1.071 | 0.75 |
| 74_W | 344_F | 1.071 | 0.75 |
| 500_F | 504_M | 1.069 | 0.75 |
| 38_E | 217_P | 1.067 | 0.75 |
| 79_W | 191_F | 1.066 | 0.75 |
| 390_R | 393_T | 1.064 | 0.75 |
| 38_E | 45_F | 1.063 | 0.74 |
| 405_L | 463_N | 1.062 | 0.74 |
| 100_T | 225_L | 1.062 | 0.74 |
| 459_G | 538_S | 1.061 | 0.74 |
| 211_G | 215_G | 1.061 | 0.74 |
| 312_T | 316_V | 1.059 | 0.74 |
| 450_L | 454_S | 1.056 | 0.74 |
| 161_S | 186_W | 1.055 | 0.74 |
| 46_Y | 157_K | 1.055 | 0.74 |
| 460_D | 464_A | 1.054 | 0.74 |
| 186_W | 460_D | 1.053 | 0.73 |
| 62_E | 70_N | 1.053 | 0.73 |
| 85_G | 159_N | 1.052 | 0.73 |
| 480_Q | 485_T | 1.048 | 0.73 |
| 15_L | 25_T | 1.048 | 0.73 |
| 437_S | 521_N | 1.044 | 0.73 |
| 334_S | 468_L | 1.042 | 0.72 |
| 283_G | 303_T | 1.041 | 0.72 |
| 88_I | 98_T | 1.040 | 0.72 |
| 17_G | 22_A | 1.039 | 0.72 |
| 333_P | 336_L | 1.037 | 0.72 |
| 265_P | 301_I | 1.035 | 0.72 |
| 187_M | 367_G | 1.034 | 0.72 |
| 545_F | 549_A | 1.034 | 0.72 |
| 33_F | 231_G | 1.034 | 0.72 |
| 212_L | 215_G | 1.032 | 0.71 |
| 173_I | 430_I | 1.029 | 0.71 |
| 79_W | 488_T | 1.028 | 0.71 |
| 50_S | 102_S | 1.025 | 0.71 |
| 353_R | 446_I | 1.024 | 0.70 |
| 107_V | 218_T | 1.023 | 0.70 |
| 10_D | 22_A | 1.022 | 0.70 |
| 81_T | 553_V | 1.020 | 0.70 |
| 129_G | 132_N | 1.018 | 0.70 |
| 46_Y | 191_F | 1.018 | 0.70 |
| 391_K | 511_K | 1.015 | 0.70 |
| 549_A | 554_Y | 1.015 | 0.70 |
| 373_S | 454_S | 1.015 | 0.70 |
| 505_I | 533_F | 1.014 | 0.69 |
| 536_V | 540_V | 1.013 | 0.69 |
| 411_I | 458_I | 1.013 | 0.69 |
| 130_V | 134_A | 1.012 | 0.69 |
| 337_W | 374_M | 1.011 | 0.69 |
| 186_W | 224_S | 1.011 | 0.69 |
| 427_M | 528_D | 1.006 | 0.69 |
| 8_T | 20_V | 1.006 | 0.69 |
| 435_I | 442_V | 1.005 | 0.68 |
| 52_L | 183_F | 1.004 | 0.68 |
| 212_L | 217_P | 1.004 | 0.68 |
| 47_G | 201_L | 1.003 | 0.68 |
| 377_S | 405_L | 1.002 | 0.68 |
| 404_R | 421_A | 1.001 | 0.68 |
| 543_G | 547_W | 1.001 | 0.68 |
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 | |
| 2xutA | 3 | 0.7427 | 100 | 0.699 | Contact Map |
| 4lepA | 2 | 0.765 | 100 | 0.736 | Contact Map |
| 4ikvA | 1 | 0.8045 | 100 | 0.751 | Contact Map |
| 4apsA | 2 | 0.7221 | 100 | 0.758 | Contact Map |
| 4j05A | 2 | 0.6792 | 100 | 0.786 | Contact Map |
| 1pw4A | 1 | 0.729 | 100 | 0.796 | Contact Map |
| 4gc0A | 1 | 0.7581 | 99.9 | 0.805 | Contact Map |
| 4ldsA | 2 | 0.7187 | 99.9 | 0.812 | Contact Map |
| 4jr9A | 1 | 0.6484 | 99.9 | 0.822 | Contact Map |
| 4m64A | 4 | 0.729 | 99.9 | 0.822 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)