| trial1 |
| ID: | 1518135843 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 543 (511) | ||
| Sequences: | 2672 (1309.9) | ||
| Seq/Len: | 5.229 | ||
| Nf(neff/√len): | 57.9 |
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: 5.229).
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 |
| 130_K | 133_E | 4.292 | 1.00 |
| 341_G | 358_E | 4.107 | 1.00 |
| 290_I | 305_A | 3.411 | 1.00 |
| 482_D | 485_E | 3.363 | 1.00 |
| 151_T | 172_E | 3.351 | 1.00 |
| 408_E | 495_K | 3.320 | 1.00 |
| 147_K | 176_E | 3.213 | 1.00 |
| 206_T | 369_I | 3.138 | 1.00 |
| 226_K | 342_L | 3.084 | 1.00 |
| 404_G | 483_M | 3.083 | 1.00 |
| 135_L | 492_L | 2.987 | 1.00 |
| 128_A | 499_I | 2.938 | 1.00 |
| 103_L | 124_Y | 2.815 | 1.00 |
| 106_K | 435_D | 2.792 | 1.00 |
| 340_A | 356_V | 2.755 | 1.00 |
| 102_E | 105_R | 2.705 | 1.00 |
| 277_K | 303_I | 2.619 | 1.00 |
| 147_K | 179_S | 2.617 | 1.00 |
| 234_L | 323_A | 2.607 | 1.00 |
| 107_A | 124_Y | 2.489 | 1.00 |
| 274_A | 278_A | 2.475 | 1.00 |
| 317_L | 356_V | 2.446 | 1.00 |
| 174_I | 384_V | 2.422 | 1.00 |
| 134_L | 414_K | 2.392 | 1.00 |
| 128_A | 503_A | 2.351 | 1.00 |
| 172_E | 176_E | 2.339 | 1.00 |
| 233_A | 332_L | 2.339 | 1.00 |
| 267_K | 271_D | 2.278 | 1.00 |
| 32_A | 101_G | 2.255 | 1.00 |
| 139_A | 492_L | 2.245 | 1.00 |
| 285_F | 356_V | 2.206 | 1.00 |
| 136_K | 496_T | 2.202 | 1.00 |
| 474_N | 477_T | 2.195 | 1.00 |
| 201_A | 205_D | 2.164 | 1.00 |
| 95_T | 498_A | 2.156 | 1.00 |
| 227_V | 230_A | 2.140 | 1.00 |
| 422_I | 430_V | 2.103 | 1.00 |
| 270_K | 274_A | 2.084 | 1.00 |
| 437_L | 499_I | 2.033 | 1.00 |
| 433_F | 503_A | 2.030 | 1.00 |
| 369_I | 377_I | 1.983 | 1.00 |
| 135_L | 496_T | 1.954 | 1.00 |
| 155_M | 168_E | 1.916 | 1.00 |
| 59_N | 64_I | 1.912 | 1.00 |
| 400_I | 489_V | 1.912 | 1.00 |
| 439_V | 443_T | 1.905 | 1.00 |
| 135_L | 407_T | 1.898 | 1.00 |
| 415_L | 430_V | 1.846 | 1.00 |
| 173_I | 206_T | 1.803 | 1.00 |
| 231_K | 339_D | 1.794 | 1.00 |
| 106_K | 109_E | 1.784 | 1.00 |
| 240_E | 289_G | 1.783 | 1.00 |
| 124_Y | 433_F | 1.781 | 1.00 |
| 263_E | 267_K | 1.774 | 1.00 |
| 231_K | 280_G | 1.763 | 1.00 |
| 318_A | 325_V | 1.738 | 1.00 |
| 103_L | 433_F | 1.736 | 1.00 |
| 402_S | 406_S | 1.727 | 1.00 |
| 285_F | 309_V | 1.720 | 1.00 |
| 197_K | 378_E | 1.706 | 1.00 |
| 410_E | 463_H | 1.692 | 1.00 |
| 474_N | 481_E | 1.690 | 1.00 |
| 176_E | 210_K | 1.689 | 1.00 |
| 130_K | 430_V | 1.686 | 1.00 |
| 298_L | 305_A | 1.686 | 1.00 |
| 407_T | 411_L | 1.686 | 1.00 |
| 131_A | 411_L | 1.682 | 1.00 |
| 306_A | 354_I | 1.682 | 1.00 |
| 124_Y | 503_A | 1.636 | 0.99 |
| 228_T | 342_L | 1.635 | 0.99 |
| 233_A | 337_L | 1.629 | 0.99 |
| 102_E | 439_V | 1.623 | 0.99 |
| 126_A | 426_E | 1.592 | 0.99 |
| 277_K | 301_E | 1.592 | 0.99 |
| 130_K | 134_L | 1.588 | 0.99 |
| 462_A | 471_A | 1.578 | 0.99 |
| 234_L | 318_A | 1.570 | 0.99 |
| 385_D | 389_G | 1.569 | 0.99 |
| 32_A | 36_R | 1.553 | 0.99 |
| 470_C | 482_D | 1.543 | 0.99 |
| 438_E | 460_R | 1.542 | 0.99 |
| 39_L | 98_V | 1.533 | 0.99 |
| 130_K | 418_Y | 1.533 | 0.99 |
| 379_E | 382_R | 1.533 | 0.99 |
| 203_I | 380_V | 1.530 | 0.99 |
| 458_K | 479_A | 1.529 | 0.99 |
| 418_Y | 430_V | 1.525 | 0.99 |
| 134_L | 137_T | 1.502 | 0.99 |
| 174_I | 387_A | 1.491 | 0.99 |
| 132_Q | 136_K | 1.489 | 0.99 |
| 450_L | 475_V | 1.486 | 0.99 |
| 60_D | 386_D | 1.465 | 0.98 |
| 259_M | 263_E | 1.460 | 0.98 |
| 180_A | 210_K | 1.458 | 0.98 |
| 94_T | 386_D | 1.456 | 0.98 |
| 431_R | 435_D | 1.451 | 0.98 |
| 276_I | 284_L | 1.451 | 0.98 |
| 130_K | 414_K | 1.445 | 0.98 |
| 346_R | 357_E | 1.419 | 0.98 |
| 320_A | 359_C | 1.389 | 0.97 |
| 122_K | 426_E | 1.369 | 0.97 |
| 93_T | 386_D | 1.364 | 0.97 |
| 226_K | 344_E | 1.363 | 0.97 |
| 494_V | 498_A | 1.363 | 0.97 |
| 37_S | 46_K | 1.353 | 0.97 |
| 450_L | 455_I | 1.351 | 0.97 |
| 441_P | 459_V | 1.351 | 0.97 |
| 140_C | 484_C | 1.346 | 0.97 |
| 124_Y | 127_A | 1.344 | 0.97 |
| 123_G | 127_A | 1.340 | 0.97 |
| 260_E | 263_E | 1.333 | 0.97 |
| 416_R | 438_E | 1.329 | 0.96 |
| 284_L | 298_L | 1.325 | 0.96 |
| 61_G | 94_T | 1.322 | 0.96 |
| 218_R | 304_V | 1.321 | 0.96 |
| 417_E | 420_E | 1.321 | 0.96 |
| 289_G | 307_R | 1.316 | 0.96 |
| 234_L | 317_L | 1.310 | 0.96 |
| 134_L | 410_E | 1.305 | 0.96 |
| 81_V | 96_A | 1.295 | 0.96 |
| 276_I | 281_A | 1.292 | 0.96 |
| 369_I | 380_V | 1.281 | 0.95 |
| 14_R | 514_D | 1.279 | 0.95 |
| 153_I | 400_I | 1.273 | 0.95 |
| 59_N | 382_R | 1.268 | 0.95 |
| 154_A | 391_V | 1.266 | 0.95 |
| 86_E | 386_D | 1.265 | 0.95 |
| 289_G | 308_R | 1.259 | 0.95 |
| 232_I | 340_A | 1.258 | 0.95 |
| 28_G | 104_L | 1.251 | 0.95 |
| 322_G | 338_G | 1.240 | 0.94 |
| 474_N | 486_N | 1.240 | 0.94 |
| 218_R | 354_I | 1.238 | 0.94 |
| 413_M | 417_E | 1.229 | 0.94 |
| 176_E | 179_S | 1.227 | 0.94 |
| 110_L | 429_A | 1.227 | 0.94 |
| 154_A | 175_V | 1.224 | 0.94 |
| 227_V | 283_V | 1.222 | 0.94 |
| 250_I | 261_F | 1.217 | 0.93 |
| 239_I | 276_I | 1.211 | 0.93 |
| 210_K | 358_E | 1.206 | 0.93 |
| 273_V | 294_A | 1.202 | 0.93 |
| 411_L | 437_L | 1.201 | 0.93 |
| 345_E | 352_S | 1.195 | 0.93 |
| 207_E | 368_L | 1.192 | 0.92 |
| 151_T | 155_M | 1.188 | 0.92 |
| 384_V | 388_V | 1.183 | 0.92 |
| 95_T | 440_I | 1.181 | 0.92 |
| 288_K | 308_R | 1.181 | 0.92 |
| 367_M | 384_V | 1.179 | 0.92 |
| 283_V | 356_V | 1.176 | 0.92 |
| 125_Q | 507_E | 1.176 | 0.92 |
| 134_L | 411_L | 1.172 | 0.92 |
| 257_K | 260_E | 1.172 | 0.92 |
| 218_R | 345_E | 1.172 | 0.92 |
| 311_K | 315_E | 1.170 | 0.92 |
| 490_E | 495_K | 1.169 | 0.91 |
| 29_R | 105_R | 1.169 | 0.91 |
| 404_G | 488_V | 1.164 | 0.91 |
| 178_V | 193_I | 1.164 | 0.91 |
| 359_C | 362_P | 1.154 | 0.91 |
| 160_G | 383_A | 1.153 | 0.91 |
| 355_F | 368_L | 1.149 | 0.91 |
| 147_K | 172_E | 1.149 | 0.91 |
| 314_M | 317_L | 1.148 | 0.91 |
| 123_G | 429_A | 1.145 | 0.90 |
| 111_L | 119_I | 1.135 | 0.90 |
| 230_A | 283_V | 1.131 | 0.90 |
| 298_L | 303_I | 1.128 | 0.89 |
| 275_E | 278_A | 1.126 | 0.89 |
| 132_Q | 496_T | 1.124 | 0.89 |
| 197_K | 381_A | 1.122 | 0.89 |
| 106_K | 436_A | 1.121 | 0.89 |
| 133_E | 136_K | 1.120 | 0.89 |
| 86_E | 93_T | 1.120 | 0.89 |
| 234_L | 325_V | 1.118 | 0.89 |
| 254_D | 257_K | 1.118 | 0.89 |
| 127_A | 430_V | 1.116 | 0.89 |
| 491_P | 494_V | 1.116 | 0.89 |
| 296_H | 300_K | 1.112 | 0.89 |
| 177_A | 208_L | 1.112 | 0.89 |
| 234_L | 314_M | 1.111 | 0.89 |
| 415_L | 434_A | 1.104 | 0.88 |
| 401_V | 492_L | 1.102 | 0.88 |
| 14_R | 17_G | 1.098 | 0.88 |
| 339_D | 360_K | 1.092 | 0.87 |
| 240_E | 291_D | 1.089 | 0.87 |
| 412_S | 416_R | 1.083 | 0.87 |
| 445_A | 450_L | 1.082 | 0.87 |
| 36_R | 446_E | 1.081 | 0.87 |
| 304_V | 354_I | 1.080 | 0.87 |
| 269_L | 293_L | 1.080 | 0.87 |
| 219_V | 295_Q | 1.079 | 0.86 |
| 138_I | 407_T | 1.075 | 0.86 |
| 401_V | 407_T | 1.075 | 0.86 |
| 416_R | 431_R | 1.074 | 0.86 |
| 220_S | 307_R | 1.074 | 0.86 |
| 40_G | 43_G | 1.073 | 0.86 |
| 229_D | 341_G | 1.064 | 0.85 |
| 76_K | 79_I | 1.061 | 0.85 |
| 225_K | 345_E | 1.056 | 0.85 |
| 150_L | 154_A | 1.056 | 0.85 |
| 27_A | 72_H | 1.055 | 0.85 |
| 59_N | 386_D | 1.050 | 0.84 |
| 44_M | 117_P | 1.049 | 0.84 |
| 444_L | 475_V | 1.045 | 0.84 |
| 147_K | 151_T | 1.043 | 0.84 |
| 99_V | 502_A | 1.041 | 0.84 |
| 439_V | 442_R | 1.040 | 0.84 |
| 100_A | 502_A | 1.039 | 0.84 |
| 61_G | 386_D | 1.039 | 0.84 |
| 229_D | 502_A | 1.039 | 0.84 |
| 173_I | 367_M | 1.038 | 0.83 |
| 283_V | 343_V | 1.037 | 0.83 |
| 32_A | 35_V | 1.032 | 0.83 |
| 341_G | 359_C | 1.032 | 0.83 |
| 128_A | 132_Q | 1.031 | 0.83 |
| 467_G | 471_A | 1.031 | 0.83 |
| 134_L | 138_I | 1.026 | 0.82 |
| 130_K | 411_L | 1.023 | 0.82 |
| 124_Y | 429_A | 1.022 | 0.82 |
| 227_V | 282_N | 1.019 | 0.82 |
| 45_D | 59_N | 1.019 | 0.82 |
| 492_L | 496_T | 1.013 | 0.81 |
| 397_D | 493_R | 1.013 | 0.81 |
| 264_Q | 267_K | 1.011 | 0.81 |
| 61_G | 93_T | 1.009 | 0.81 |
| 114_N | 117_P | 1.008 | 0.81 |
| 281_A | 337_L | 1.007 | 0.81 |
| 168_E | 172_E | 1.006 | 0.81 |
| 39_L | 95_T | 1.006 | 0.81 |
| 410_E | 414_K | 1.005 | 0.81 |
| 61_G | 90_G | 1.002 | 0.80 |
| 177_A | 181_V | 1.000 | 0.80 |
| 160_G | 164_E | 1.000 | 0.80 |
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 | |
| 3ruvA | 4 | 0.9503 | 100 | 0.021 | Contact Map |
| 3j1bA | 16 | 0.9319 | 100 | 0.039 | Contact Map |
| 1q3qA | 4 | 0.9466 | 100 | 0.045 | Contact Map |
| 1a6dA | 1 | 0.9208 | 100 | 0.066 | Contact Map |
| 3p9dG | 2 | 0.9319 | 100 | 0.091 | Contact Map |
| 3ko1A | 9 | 0.9245 | 100 | 0.093 | Contact Map |
| 1a6dB | 1 | 0.919 | 100 | 0.104 | Contact Map |
| 3p9dA | 2 | 0.9632 | 100 | 0.111 | Contact Map |
| 3p9dD | 2 | 0.9429 | 100 | 0.114 | Contact Map |
| 3iygA | 1 | 0.9411 | 100 | 0.12 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)