| 1010 |
| ID: | 1430253691 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 622 (472) | ||
| Sequences: | 945 (607.2) | ||
| Seq/Len: | 2.002 | ||
| Nf(neff/√len): | 27.9 |
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: 2.002).
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 |
| 209_F | 382_P | 3.216 | 1.00 |
| 418_K | 421_Q | 3.190 | 1.00 |
| 240_C | 304_I | 3.001 | 1.00 |
| 340_V | 349_E | 2.886 | 1.00 |
| 418_K | 422_E | 2.813 | 1.00 |
| 107_M | 391_V | 2.555 | 1.00 |
| 393_R | 473_D | 2.515 | 1.00 |
| 48_T | 71_G | 2.475 | 1.00 |
| 247_H | 251_T | 2.391 | 1.00 |
| 153_L | 245_L | 2.351 | 1.00 |
| 67_C | 71_G | 2.250 | 1.00 |
| 362_P | 365_R | 2.182 | 1.00 |
| 187_F | 285_E | 2.157 | 0.99 |
| 61_I | 65_A | 2.150 | 0.99 |
| 52_L | 67_C | 2.122 | 0.99 |
| 128_L | 210_L | 2.099 | 0.99 |
| 234_I | 481_V | 2.030 | 0.99 |
| 384_S | 387_A | 2.022 | 0.99 |
| 114_Y | 214_R | 1.986 | 0.99 |
| 407_A | 466_S | 1.939 | 0.99 |
| 406_T | 472_G | 1.936 | 0.99 |
| 264_L | 277_P | 1.931 | 0.99 |
| 244_G | 247_H | 1.927 | 0.99 |
| 132_V | 308_T | 1.910 | 0.98 |
| 15_R | 18_V | 1.894 | 0.98 |
| 126_D | 441_K | 1.877 | 0.98 |
| 214_R | 481_V | 1.876 | 0.98 |
| 236_V | 308_T | 1.874 | 0.98 |
| 417_T | 421_Q | 1.871 | 0.98 |
| 131_A | 311_V | 1.836 | 0.98 |
| 388_G | 477_R | 1.834 | 0.98 |
| 359_R | 377_Q | 1.831 | 0.98 |
| 125_V | 482_C | 1.826 | 0.98 |
| 89_D | 348_R | 1.814 | 0.98 |
| 132_V | 304_I | 1.797 | 0.97 |
| 161_V | 166_A | 1.785 | 0.97 |
| 92_L | 287_Y | 1.781 | 0.97 |
| 79_V | 97_V | 1.744 | 0.97 |
| 393_R | 475_V | 1.734 | 0.97 |
| 414_M | 419_A | 1.727 | 0.97 |
| 249_T | 293_A | 1.718 | 0.96 |
| 458_D | 461_E | 1.714 | 0.96 |
| 423_Y | 452_A | 1.686 | 0.96 |
| 380_I | 391_V | 1.664 | 0.96 |
| 45_D | 48_T | 1.658 | 0.95 |
| 213_Q | 237_L | 1.634 | 0.95 |
| 20_E | 30_P | 1.633 | 0.95 |
| 52_L | 65_A | 1.630 | 0.95 |
| 425_G | 449_A | 1.609 | 0.94 |
| 217_D | 231_A | 1.603 | 0.94 |
| 336_A | 483_N | 1.593 | 0.94 |
| 399_L | 404_G | 1.588 | 0.94 |
| 20_E | 32_R | 1.582 | 0.94 |
| 432_L | 483_N | 1.579 | 0.94 |
| 108_M | 238_I | 1.575 | 0.93 |
| 387_A | 390_Y | 1.566 | 0.93 |
| 281_E | 285_E | 1.566 | 0.93 |
| 127_A | 314_D | 1.556 | 0.93 |
| 280_S | 283_A | 1.554 | 0.93 |
| 104_G | 301_R | 1.554 | 0.93 |
| 78_P | 81_G | 1.542 | 0.93 |
| 115_E | 232_D | 1.526 | 0.92 |
| 31_A | 52_L | 1.523 | 0.92 |
| 260_E | 282_L | 1.519 | 0.92 |
| 128_L | 308_T | 1.513 | 0.92 |
| 221_D | 225_E | 1.506 | 0.91 |
| 150_E | 193_K | 1.505 | 0.91 |
| 36_S | 461_E | 1.499 | 0.91 |
| 214_R | 479_F | 1.497 | 0.91 |
| 114_Y | 118_Q | 1.489 | 0.91 |
| 108_M | 305_M | 1.483 | 0.90 |
| 203_L | 210_L | 1.469 | 0.90 |
| 106_R | 330_D | 1.458 | 0.89 |
| 290_M | 336_A | 1.438 | 0.89 |
| 54_N | 270_D | 1.438 | 0.89 |
| 35_A | 43_I | 1.431 | 0.88 |
| 173_H | 371_A | 1.425 | 0.88 |
| 364_G | 373_A | 1.424 | 0.88 |
| 459_V | 463_V | 1.416 | 0.88 |
| 467_D | 474_K | 1.403 | 0.87 |
| 378_P | 393_R | 1.401 | 0.87 |
| 62_T | 350_L | 1.395 | 0.87 |
| 464_R | 474_K | 1.385 | 0.86 |
| 86_D | 348_R | 1.373 | 0.85 |
| 229_L | 391_V | 1.372 | 0.85 |
| 31_A | 65_A | 1.370 | 0.85 |
| 14_V | 20_E | 1.366 | 0.85 |
| 337_K | 359_R | 1.365 | 0.85 |
| 55_A | 96_A | 1.351 | 0.84 |
| 40_L | 48_T | 1.343 | 0.84 |
| 257_I | 365_R | 1.338 | 0.83 |
| 260_E | 264_L | 1.337 | 0.83 |
| 47_K | 418_K | 1.337 | 0.83 |
| 114_Y | 481_V | 1.327 | 0.83 |
| 81_G | 353_H | 1.318 | 0.82 |
| 395_G | 473_D | 1.312 | 0.82 |
| 109_T | 326_R | 1.309 | 0.81 |
| 338_K | 349_E | 1.301 | 0.81 |
| 51_Q | 74_G | 1.297 | 0.81 |
| 55_A | 77_F | 1.290 | 0.80 |
| 223_V | 227_F | 1.275 | 0.79 |
| 74_G | 101_I | 1.272 | 0.79 |
| 114_Y | 232_D | 1.260 | 0.78 |
| 18_V | 34_L | 1.255 | 0.77 |
| 102_N | 298_W | 1.254 | 0.77 |
| 155_R | 162_D | 1.240 | 0.76 |
| 363_A | 395_G | 1.235 | 0.76 |
| 227_F | 375_V | 1.234 | 0.76 |
| 78_P | 353_H | 1.230 | 0.75 |
| 383_G | 389_S | 1.229 | 0.75 |
| 278_A | 351_Y | 1.226 | 0.75 |
| 121_E | 482_C | 1.215 | 0.74 |
| 390_Y | 459_V | 1.210 | 0.74 |
| 420_K | 446_A | 1.210 | 0.74 |
| 60_G | 93_S | 1.209 | 0.74 |
| 136_L | 205_S | 1.208 | 0.74 |
| 132_V | 311_V | 1.204 | 0.73 |
| 47_K | 50_E | 1.203 | 0.73 |
| 460_D | 463_V | 1.197 | 0.73 |
| 157_M | 166_A | 1.195 | 0.72 |
| 35_A | 45_D | 1.192 | 0.72 |
| 383_G | 386_G | 1.190 | 0.72 |
| 117_L | 316_F | 1.188 | 0.72 |
| 440_V | 448_V | 1.185 | 0.72 |
| 80_G | 98_G | 1.182 | 0.71 |
| 137_G | 244_G | 1.174 | 0.70 |
| 55_A | 65_A | 1.170 | 0.70 |
| 340_V | 347_E | 1.163 | 0.69 |
| 343_V | 350_L | 1.161 | 0.69 |
| 195_R | 248_Q | 1.160 | 0.69 |
| 278_A | 287_Y | 1.158 | 0.69 |
| 365_R | 373_A | 1.157 | 0.69 |
| 287_Y | 351_Y | 1.154 | 0.69 |
| 432_L | 450_E | 1.145 | 0.68 |
| 69_P | 100_D | 1.136 | 0.67 |
| 157_M | 174_C | 1.135 | 0.67 |
| 283_A | 358_T | 1.134 | 0.67 |
| 157_M | 299_V | 1.132 | 0.66 |
| 77_F | 96_A | 1.132 | 0.66 |
| 216_T | 479_F | 1.129 | 0.66 |
| 369_P | 372_Y | 1.122 | 0.65 |
| 127_A | 130_E | 1.118 | 0.65 |
| 19_W | 22_P | 1.114 | 0.65 |
| 74_G | 98_G | 1.113 | 0.65 |
| 423_Y | 454_G | 1.109 | 0.64 |
| 18_V | 401_L | 1.109 | 0.64 |
| 287_Y | 291_C | 1.106 | 0.64 |
| 410_A | 459_V | 1.106 | 0.64 |
| 75_Y | 99_Y | 1.102 | 0.63 |
| 309_R | 312_F | 1.102 | 0.63 |
| 281_E | 400_D | 1.095 | 0.63 |
| 158_R | 179_F | 1.093 | 0.62 |
| 388_G | 432_L | 1.093 | 0.62 |
| 391_V | 478_T | 1.092 | 0.62 |
| 113_T | 233_Q | 1.087 | 0.62 |
| 279_G | 284_E | 1.086 | 0.62 |
| 238_I | 305_M | 1.086 | 0.62 |
| 173_H | 372_Y | 1.086 | 0.62 |
| 209_F | 381_I | 1.080 | 0.61 |
| 378_P | 475_V | 1.077 | 0.61 |
| 260_E | 263_D | 1.074 | 0.60 |
| 461_E | 464_R | 1.073 | 0.60 |
| 214_R | 234_I | 1.072 | 0.60 |
| 127_A | 311_V | 1.069 | 0.60 |
| 72_H | 98_G | 1.069 | 0.60 |
| 69_P | 74_G | 1.063 | 0.59 |
| 111_N | 233_Q | 1.062 | 0.59 |
| 238_I | 287_Y | 1.061 | 0.59 |
| 77_F | 81_G | 1.060 | 0.59 |
| 94_P | 209_F | 1.059 | 0.59 |
| 298_W | 302_Q | 1.057 | 0.59 |
| 14_V | 18_V | 1.056 | 0.59 |
| 134_S | 199_Q | 1.056 | 0.59 |
| 77_F | 450_E | 1.055 | 0.58 |
| 383_G | 459_V | 1.053 | 0.58 |
| 423_Y | 428_V | 1.053 | 0.58 |
| 339_E | 352_V | 1.051 | 0.58 |
| 20_E | 365_R | 1.051 | 0.58 |
| 83_G | 96_A | 1.048 | 0.58 |
| 125_V | 129_F | 1.047 | 0.58 |
| 386_G | 389_S | 1.046 | 0.57 |
| 74_G | 100_D | 1.043 | 0.57 |
| 107_M | 235_V | 1.038 | 0.57 |
| 332_A | 335_I | 1.038 | 0.57 |
| 257_I | 276_A | 1.037 | 0.56 |
| 210_L | 308_T | 1.036 | 0.56 |
| 37_E | 40_L | 1.036 | 0.56 |
| 76_G | 273_L | 1.035 | 0.56 |
| 110_T | 234_I | 1.033 | 0.56 |
| 241_G | 356_G | 1.032 | 0.56 |
| 75_Y | 247_H | 1.031 | 0.56 |
| 47_K | 73_Q | 1.030 | 0.56 |
| 62_T | 348_R | 1.029 | 0.56 |
| 217_D | 477_R | 1.028 | 0.55 |
| 92_L | 249_T | 1.027 | 0.55 |
| 134_S | 205_S | 1.027 | 0.55 |
| 368_L | 405_S | 1.026 | 0.55 |
| 360_A | 398_S | 1.026 | 0.55 |
| 463_V | 472_G | 1.026 | 0.55 |
| 57_H | 281_E | 1.024 | 0.55 |
| 311_V | 315_V | 1.021 | 0.55 |
| 157_M | 161_V | 1.021 | 0.55 |
| 48_T | 51_Q | 1.021 | 0.55 |
| 253_Y | 289_A | 1.021 | 0.55 |
| 48_T | 52_L | 1.018 | 0.54 |
| 46_D | 49_L | 1.018 | 0.54 |
| 238_I | 301_R | 1.018 | 0.54 |
| 263_D | 282_L | 1.017 | 0.54 |
| 343_V | 346_E | 1.015 | 0.54 |
| 60_G | 90_G | 1.012 | 0.54 |
| 227_F | 393_R | 1.010 | 0.53 |
| 129_F | 304_I | 1.006 | 0.53 |
| 410_A | 453_P | 1.005 | 0.53 |
| 58_L | 84_A | 1.005 | 0.53 |
| 55_A | 83_G | 1.001 | 0.52 |
| 256_R | 282_L | 1.000 | 0.52 |
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 | |
| 4dwrB | 3 | 0.7781 | 100 | 0.28 | Contact Map |
| 2epgA | 2 | 0.7074 | 100 | 0.292 | Contact Map |
| 1jw3A | 1 | 0.2203 | 100 | 0.837 | Contact Map |
| 4n2pA | 4 | 0.2219 | 100 | 0.839 | Contact Map |
| 1j5uA | 1 | 0.1994 | 100 | 0.873 | Contact Map |
| 3gkuA | 3 | 0.1929 | 56.6 | 0.983 | Contact Map |
| 3awdA | 4 | 0.373 | 41.8 | 0.984 | Contact Map |
| 1wv8A | 1 | 0.1125 | 31.5 | 0.985 | Contact Map |
| 4q9nA | 8 | 0.4084 | 26.2 | 0.986 | Contact Map |
| 3btnA | 2 | 0.3023 | 22.6 | 0.986 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)