| serinc |
| ID: | 1507038524 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 465 (457) | ||
| Sequences: | 843 (451) | ||
| Seq/Len: | 1.845 | ||
| Nf(neff/√len): | 21.1 |
Jackhmmer Results: (2016_04)
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: 1.845).
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 |
| 229_Y | 246_S | 3.487 | 1.00 |
| 243_F | 247_I | 3.458 | 1.00 |
| 192_L | 196_W | 3.044 | 1.00 |
| 226_T | 230_I | 2.721 | 1.00 |
| 223_T | 227_L | 2.537 | 1.00 |
| 247_I | 251_F | 2.392 | 1.00 |
| 258_I | 450_G | 2.215 | 1.00 |
| 246_S | 250_I | 2.188 | 0.99 |
| 343_I | 346_N | 1.982 | 0.99 |
| 219_I | 223_T | 1.937 | 0.98 |
| 220_L | 281_L | 1.887 | 0.98 |
| 119_S | 402_L | 1.849 | 0.98 |
| 248_N | 442_S | 1.833 | 0.97 |
| 241_N | 294_N | 1.825 | 0.97 |
| 196_W | 209_A | 1.820 | 0.97 |
| 221_S | 280_T | 1.815 | 0.97 |
| 432_E | 435_M | 1.806 | 0.97 |
| 294_N | 435_M | 1.798 | 0.97 |
| 314_T | 318_A | 1.781 | 0.97 |
| 395_Y | 401_H | 1.774 | 0.97 |
| 218_Y | 256_S | 1.768 | 0.97 |
| 294_N | 432_E | 1.731 | 0.96 |
| 451_W | 456_P | 1.675 | 0.95 |
| 311_G | 315_T | 1.661 | 0.95 |
| 48_V | 448_I | 1.652 | 0.95 |
| 136_Q | 193_A | 1.644 | 0.94 |
| 258_I | 261_L | 1.642 | 0.94 |
| 271_S | 275_Q | 1.604 | 0.93 |
| 272_G | 275_Q | 1.604 | 0.93 |
| 255_I | 450_G | 1.575 | 0.92 |
| 209_A | 213_V | 1.567 | 0.92 |
| 224_G | 228_L | 1.553 | 0.92 |
| 15_M | 20_T | 1.551 | 0.92 |
| 109_F | 162_F | 1.549 | 0.92 |
| 18_G | 22_A | 1.546 | 0.92 |
| 17_C | 23_S | 1.540 | 0.91 |
| 6_G | 9_S | 1.538 | 0.91 |
| 20_T | 23_S | 1.537 | 0.91 |
| 355_S | 358_S | 1.532 | 0.91 |
| 413_M | 418_W | 1.523 | 0.91 |
| 255_I | 446_V | 1.520 | 0.91 |
| 17_C | 20_T | 1.513 | 0.90 |
| 126_K | 130_D | 1.513 | 0.90 |
| 15_M | 18_G | 1.511 | 0.90 |
| 15_M | 22_A | 1.507 | 0.90 |
| 140_W | 143_K | 1.505 | 0.90 |
| 222_L | 226_T | 1.504 | 0.90 |
| 455_A | 462_R | 1.503 | 0.90 |
| 6_G | 11_A | 1.503 | 0.90 |
| 240_I | 243_F | 1.496 | 0.90 |
| 342_C | 345_Y | 1.485 | 0.89 |
| 32_C | 37_S | 1.478 | 0.89 |
| 342_C | 346_N | 1.478 | 0.89 |
| 354_V | 357_I | 1.471 | 0.89 |
| 286_L | 289_S | 1.446 | 0.88 |
| 451_W | 455_A | 1.440 | 0.87 |
| 9_S | 13_C | 1.440 | 0.87 |
| 287_T | 439_I | 1.436 | 0.87 |
| 410_Y | 418_W | 1.430 | 0.87 |
| 157_I | 162_F | 1.425 | 0.86 |
| 367_L | 370_A | 1.417 | 0.86 |
| 18_G | 23_S | 1.409 | 0.86 |
| 246_S | 249_L | 1.408 | 0.86 |
| 17_C | 22_A | 1.407 | 0.86 |
| 39_R | 132_R | 1.400 | 0.85 |
| 15_M | 19_G | 1.386 | 0.84 |
| 227_L | 230_I | 1.385 | 0.84 |
| 244_F | 435_M | 1.384 | 0.84 |
| 436_W | 443_W | 1.382 | 0.84 |
| 95_C | 170_G | 1.379 | 0.84 |
| 455_A | 464_F | 1.375 | 0.84 |
| 451_W | 462_R | 1.375 | 0.84 |
| 250_I | 254_A | 1.367 | 0.83 |
| 192_L | 209_A | 1.350 | 0.82 |
| 245_I | 259_S | 1.350 | 0.82 |
| 133_S | 392_G | 1.339 | 0.81 |
| 6_G | 10_A | 1.330 | 0.81 |
| 173_G | 409_L | 1.330 | 0.81 |
| 373_D | 378_T | 1.329 | 0.81 |
| 116_A | 405_V | 1.328 | 0.81 |
| 22_A | 25_C | 1.319 | 0.80 |
| 117_L | 146_I | 1.311 | 0.80 |
| 35_A | 38_S | 1.307 | 0.79 |
| 12_Q | 15_M | 1.306 | 0.79 |
| 222_L | 250_I | 1.296 | 0.78 |
| 329_D | 333_I | 1.295 | 0.78 |
| 144_F | 335_G | 1.293 | 0.78 |
| 22_A | 40_F | 1.290 | 0.78 |
| 441_S | 445_G | 1.283 | 0.77 |
| 248_N | 287_T | 1.282 | 0.77 |
| 420_K | 444_L | 1.281 | 0.77 |
| 199_S | 228_L | 1.276 | 0.77 |
| 452_S | 459_L | 1.274 | 0.77 |
| 48_V | 335_G | 1.273 | 0.77 |
| 123_L | 126_K | 1.266 | 0.76 |
| 238_C | 299_C | 1.258 | 0.75 |
| 453_L | 456_P | 1.250 | 0.75 |
| 350_S | 354_V | 1.248 | 0.75 |
| 224_G | 284_V | 1.239 | 0.74 |
| 149_G | 454_A | 1.231 | 0.73 |
| 179_L | 183_V | 1.226 | 0.73 |
| 216_L | 447_F | 1.226 | 0.73 |
| 41_M | 45_I | 1.224 | 0.73 |
| 12_Q | 18_G | 1.219 | 0.72 |
| 289_S | 438_K | 1.217 | 0.72 |
| 22_A | 42_Y | 1.207 | 0.71 |
| 14_A | 17_C | 1.200 | 0.70 |
| 158_P | 335_G | 1.197 | 0.70 |
| 116_A | 223_T | 1.195 | 0.70 |
| 149_G | 153_G | 1.185 | 0.69 |
| 366_V | 369_E | 1.182 | 0.69 |
| 165_A | 169_V | 1.176 | 0.68 |
| 112_A | 405_V | 1.175 | 0.68 |
| 241_N | 397_W | 1.174 | 0.68 |
| 365_R | 369_E | 1.171 | 0.68 |
| 18_G | 26_C | 1.170 | 0.68 |
| 329_D | 332_N | 1.170 | 0.68 |
| 133_S | 277_S | 1.167 | 0.67 |
| 26_C | 30_P | 1.167 | 0.67 |
| 399_M | 418_W | 1.166 | 0.67 |
| 113_C | 154_A | 1.165 | 0.67 |
| 210_L | 214_T | 1.162 | 0.67 |
| 190_H | 277_S | 1.160 | 0.67 |
| 13_C | 22_A | 1.159 | 0.67 |
| 18_G | 28_A | 1.158 | 0.67 |
| 240_I | 244_F | 1.157 | 0.66 |
| 145_L | 148_F | 1.156 | 0.66 |
| 252_C | 280_T | 1.155 | 0.66 |
| 345_Y | 348_I | 1.152 | 0.66 |
| 171_L | 180_V | 1.152 | 0.66 |
| 333_I | 337_V | 1.150 | 0.66 |
| 49_G | 111_M | 1.148 | 0.66 |
| 315_T | 318_A | 1.147 | 0.65 |
| 14_A | 20_T | 1.143 | 0.65 |
| 175_L | 399_M | 1.141 | 0.65 |
| 118_M | 186_V | 1.139 | 0.65 |
| 13_C | 23_S | 1.136 | 0.64 |
| 459_L | 464_F | 1.136 | 0.64 |
| 313_A | 316_T | 1.135 | 0.64 |
| 119_S | 350_S | 1.126 | 0.63 |
| 38_S | 133_S | 1.124 | 0.63 |
| 313_A | 322_H | 1.120 | 0.63 |
| 343_I | 347_C | 1.120 | 0.63 |
| 8_C | 12_Q | 1.118 | 0.63 |
| 16_C | 20_T | 1.115 | 0.62 |
| 233_T | 342_C | 1.113 | 0.62 |
| 286_L | 445_G | 1.112 | 0.62 |
| 114_F | 173_G | 1.109 | 0.62 |
| 17_C | 37_S | 1.109 | 0.62 |
| 250_I | 257_V | 1.109 | 0.62 |
| 275_Q | 282_Y | 1.108 | 0.62 |
| 52_L | 118_M | 1.107 | 0.61 |
| 265_Q | 455_A | 1.106 | 0.61 |
| 409_L | 412_M | 1.102 | 0.61 |
| 14_A | 461_N | 1.098 | 0.60 |
| 168_W | 217_C | 1.076 | 0.58 |
| 214_T | 457_I | 1.075 | 0.58 |
| 364_K | 367_L | 1.075 | 0.58 |
| 39_R | 389_E | 1.073 | 0.58 |
| 386_T | 411_V | 1.072 | 0.58 |
| 116_A | 119_S | 1.072 | 0.58 |
| 126_K | 285_Y | 1.070 | 0.58 |
| 181_Q | 274_L | 1.070 | 0.58 |
| 29_C | 35_A | 1.067 | 0.57 |
| 448_I | 454_A | 1.063 | 0.57 |
| 271_S | 293_N | 1.062 | 0.57 |
| 456_P | 462_R | 1.062 | 0.57 |
| 361_N | 370_A | 1.058 | 0.56 |
| 169_V | 199_S | 1.058 | 0.56 |
| 276_S | 286_L | 1.055 | 0.56 |
| 95_C | 412_M | 1.051 | 0.55 |
| 318_A | 321_T | 1.051 | 0.55 |
| 127_S | 298_E | 1.051 | 0.55 |
| 40_F | 135_I | 1.051 | 0.55 |
| 21_A | 26_C | 1.050 | 0.55 |
| 45_I | 144_F | 1.050 | 0.55 |
| 268_L | 463_D | 1.046 | 0.55 |
| 249_L | 254_A | 1.045 | 0.55 |
| 232_F | 430_G | 1.044 | 0.55 |
| 267_R | 457_I | 1.043 | 0.55 |
| 365_R | 370_A | 1.042 | 0.54 |
| 283_T | 446_V | 1.042 | 0.54 |
| 452_S | 462_R | 1.042 | 0.54 |
| 25_C | 385_S | 1.041 | 0.54 |
| 295_P | 432_E | 1.041 | 0.54 |
| 129_R | 276_S | 1.038 | 0.54 |
| 459_L | 462_R | 1.037 | 0.54 |
| 14_A | 23_S | 1.033 | 0.54 |
| 83_L | 87_S | 1.033 | 0.54 |
| 136_Q | 432_E | 1.032 | 0.53 |
| 295_P | 438_K | 1.032 | 0.53 |
| 10_A | 13_C | 1.031 | 0.53 |
| 167_M | 431_N | 1.030 | 0.53 |
| 45_I | 147_C | 1.027 | 0.53 |
| 183_V | 453_L | 1.026 | 0.53 |
| 229_Y | 236_T | 1.026 | 0.53 |
| 195_N | 199_S | 1.026 | 0.53 |
| 227_L | 231_Y | 1.022 | 0.52 |
| 215_L | 219_I | 1.022 | 0.52 |
| 311_G | 318_A | 1.021 | 0.52 |
| 176_A | 346_N | 1.021 | 0.52 |
| 186_V | 446_V | 1.020 | 0.52 |
| 210_L | 265_Q | 1.019 | 0.52 |
| 14_A | 32_C | 1.019 | 0.52 |
| 223_T | 276_S | 1.018 | 0.52 |
| 188_F | 192_L | 1.015 | 0.52 |
| 98_A | 193_A | 1.014 | 0.51 |
| 332_N | 339_W | 1.012 | 0.51 |
| 129_R | 398_S | 1.012 | 0.51 |
| 287_T | 442_S | 1.009 | 0.51 |
| 243_F | 250_I | 1.006 | 0.51 |
| 451_W | 464_F | 1.006 | 0.51 |
| 24_M | 30_P | 1.005 | 0.50 |
| 260_I | 373_D | 1.001 | 0.50 |
| 193_A | 274_L | 1.001 | 0.50 |
| 16_C | 24_M | 1.001 | 0.50 |
| 110_G | 150_A | 1.001 | 0.50 |
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 | |
| 4ymkA | 2 | 0 | 9.8 | 0.983 | Contact Map |
| 3j1rA | 21 | 0.0559 | 8.7 | 0.983 | Contact Map |
| 4zw9A | 1 | 0 | 4.5 | 0.985 | Contact Map |
| 4he8A | 2 | 0.1914 | 4.1 | 0.985 | Contact Map |
| 3dl8E | 2 | 0.1376 | 4.1 | 0.985 | Contact Map |
| 4k5yA | 3 | 0.4925 | 3.9 | 0.986 | Contact Map |
| 4pypA | 1 | 0.6409 | 2.8 | 0.987 | Contact Map |
| 4mzzA | 2 | 0.0688 | 2.4 | 0.987 | Contact Map |
| 3rkoA | 2 | 0.1957 | 2.1 | 0.987 | Contact Map |
| 4bgnA | 2 | 0.4108 | 2 | 0.988 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)