| vim |
| ID: | 1486041751 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 466 (445) | ||
| Sequences: | 3566 (1990.3) | ||
| Seq/Len: | 8.013 | ||
| Nf(neff/√len): | 94.3 |
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: 8.013).
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 |
| 53_Y | 56_S | 2.031 | 1.00 |
| 85_D | 89_A | 1.984 | 1.00 |
| 87_S | 91_A | 1.893 | 1.00 |
| 189_L | 193_M | 1.881 | 1.00 |
| 61_Y | 64_R | 1.875 | 1.00 |
| 25_S | 29_S | 1.851 | 1.00 |
| 82_D | 89_A | 1.844 | 1.00 |
| 24_P | 28_R | 1.841 | 1.00 |
| 82_D | 85_D | 1.836 | 1.00 |
| 375_E | 378_R | 1.765 | 1.00 |
| 33_T | 37_T | 1.750 | 1.00 |
| 36_R | 39_S | 1.698 | 1.00 |
| 85_D | 93_N | 1.698 | 1.00 |
| 337_N | 341_E | 1.697 | 1.00 |
| 450_R | 455_I | 1.692 | 1.00 |
| 52_L | 56_S | 1.687 | 1.00 |
| 85_D | 91_A | 1.682 | 1.00 |
| 63_T | 67_A | 1.655 | 1.00 |
| 35_T | 39_S | 1.639 | 1.00 |
| 346_E | 349_E | 1.626 | 1.00 |
| 66_S | 69_R | 1.615 | 1.00 |
| 81_Q | 84_V | 1.602 | 1.00 |
| 130_I | 134_E | 1.593 | 1.00 |
| 32_T | 36_R | 1.593 | 1.00 |
| 49_S | 53_Y | 1.579 | 1.00 |
| 267_A | 271_D | 1.575 | 1.00 |
| 87_S | 90_D | 1.574 | 1.00 |
| 75_P | 79_L | 1.574 | 1.00 |
| 68_V | 71_R | 1.570 | 1.00 |
| 65_S | 69_R | 1.567 | 1.00 |
| 32_T | 35_T | 1.562 | 1.00 |
| 28_R | 32_T | 1.556 | 1.00 |
| 84_V | 87_S | 1.550 | 1.00 |
| 27_S | 30_Y | 1.548 | 1.00 |
| 53_Y | 57_P | 1.532 | 1.00 |
| 56_S | 60_V | 1.528 | 1.00 |
| 318_E | 321_R | 1.522 | 1.00 |
| 57_P | 60_V | 1.518 | 1.00 |
| 208_Q | 212_N | 1.514 | 1.00 |
| 82_D | 91_A | 1.493 | 0.99 |
| 68_V | 72_S | 1.487 | 0.99 |
| 74_V | 78_R | 1.484 | 0.99 |
| 81_Q | 85_D | 1.478 | 0.99 |
| 84_V | 89_A | 1.477 | 0.99 |
| 221_E | 225_E | 1.476 | 0.99 |
| 33_T | 36_R | 1.449 | 0.99 |
| 407_E | 410_R | 1.444 | 0.99 |
| 34_S | 38_Y | 1.428 | 0.99 |
| 56_S | 59_G | 1.427 | 0.99 |
| 76_G | 79_L | 1.425 | 0.99 |
| 57_P | 61_Y | 1.403 | 0.99 |
| 45_R | 48_T | 1.398 | 0.99 |
| 33_T | 38_Y | 1.396 | 0.99 |
| 82_D | 87_S | 1.390 | 0.99 |
| 38_Y | 41_G | 1.388 | 0.99 |
| 80_L | 84_V | 1.387 | 0.99 |
| 72_S | 76_G | 1.385 | 0.99 |
| 28_R | 31_V | 1.359 | 0.99 |
| 48_T | 52_L | 1.356 | 0.99 |
| 290_W | 294_K | 1.355 | 0.99 |
| 76_G | 80_L | 1.347 | 0.99 |
| 288_E | 292_K | 1.346 | 0.99 |
| 37_T | 40_L | 1.345 | 0.99 |
| 54_A | 60_V | 1.341 | 0.99 |
| 26_S | 30_Y | 1.332 | 0.99 |
| 84_V | 91_A | 1.331 | 0.99 |
| 66_S | 71_R | 1.326 | 0.99 |
| 78_R | 81_Q | 1.324 | 0.99 |
| 431_L | 434_V | 1.320 | 0.98 |
| 60_V | 64_R | 1.319 | 0.98 |
| 27_S | 32_T | 1.317 | 0.98 |
| 53_Y | 60_V | 1.316 | 0.98 |
| 415_L | 418_F | 1.315 | 0.98 |
| 71_R | 75_P | 1.313 | 0.98 |
| 273_R | 277_E | 1.312 | 0.98 |
| 38_Y | 42_S | 1.312 | 0.98 |
| 62_A | 65_S | 1.312 | 0.98 |
| 50_R | 53_Y | 1.304 | 0.98 |
| 211_D | 214_S | 1.300 | 0.98 |
| 53_Y | 61_Y | 1.297 | 0.98 |
| 98_N | 101_T | 1.289 | 0.98 |
| 29_S | 38_Y | 1.287 | 0.98 |
| 66_S | 72_S | 1.284 | 0.98 |
| 430_S | 435_D | 1.276 | 0.98 |
| 59_G | 63_T | 1.273 | 0.98 |
| 443_L | 447_V | 1.270 | 0.98 |
| 69_R | 73_S | 1.265 | 0.98 |
| 452_G | 455_I | 1.264 | 0.98 |
| 40_L | 44_L | 1.264 | 0.98 |
| 30_Y | 33_T | 1.250 | 0.98 |
| 26_S | 33_T | 1.248 | 0.98 |
| 79_L | 83_S | 1.245 | 0.98 |
| 31_V | 35_T | 1.245 | 0.98 |
| 51_S | 64_R | 1.241 | 0.97 |
| 23_R | 27_S | 1.239 | 0.97 |
| 48_T | 51_S | 1.237 | 0.97 |
| 86_F | 89_A | 1.236 | 0.97 |
| 71_R | 74_V | 1.235 | 0.97 |
| 123_F | 127_Q | 1.234 | 0.97 |
| 121_V | 124_L | 1.233 | 0.97 |
| 43_A | 50_R | 1.231 | 0.97 |
| 426_T | 429_D | 1.226 | 0.97 |
| 444_I | 449_T | 1.219 | 0.97 |
| 433_L | 437_H | 1.219 | 0.97 |
| 434_V | 437_H | 1.217 | 0.97 |
| 37_T | 41_G | 1.216 | 0.97 |
| 86_F | 91_A | 1.214 | 0.97 |
| 24_P | 29_S | 1.214 | 0.97 |
| 41_G | 46_P | 1.213 | 0.97 |
| 429_D | 432_P | 1.212 | 0.97 |
| 46_P | 50_R | 1.211 | 0.97 |
| 69_R | 72_S | 1.211 | 0.97 |
| 217_R | 221_E | 1.209 | 0.97 |
| 36_R | 41_G | 1.209 | 0.97 |
| 30_Y | 38_Y | 1.207 | 0.97 |
| 435_D | 438_S | 1.206 | 0.97 |
| 29_S | 33_T | 1.203 | 0.97 |
| 48_T | 55_S | 1.203 | 0.97 |
| 219_D | 223_K | 1.203 | 0.97 |
| 275_Q | 348_E | 1.199 | 0.97 |
| 445_K | 449_T | 1.196 | 0.97 |
| 435_D | 440_R | 1.195 | 0.97 |
| 430_S | 433_L | 1.195 | 0.97 |
| 49_S | 52_L | 1.194 | 0.97 |
| 422_N | 426_T | 1.193 | 0.97 |
| 44_L | 47_S | 1.192 | 0.97 |
| 167_D | 170_R | 1.189 | 0.97 |
| 338_E | 342_R | 1.188 | 0.96 |
| 25_S | 28_R | 1.187 | 0.96 |
| 54_A | 58_G | 1.184 | 0.96 |
| 372_M | 375_E | 1.180 | 0.96 |
| 44_L | 48_T | 1.178 | 0.96 |
| 52_L | 59_G | 1.175 | 0.96 |
| 61_Y | 67_A | 1.172 | 0.96 |
| 62_A | 66_S | 1.171 | 0.96 |
| 29_S | 32_T | 1.170 | 0.96 |
| 438_S | 443_L | 1.170 | 0.96 |
| 438_S | 442_L | 1.170 | 0.96 |
| 41_G | 45_R | 1.170 | 0.96 |
| 28_R | 33_T | 1.169 | 0.96 |
| 79_L | 82_D | 1.168 | 0.96 |
| 42_S | 45_R | 1.168 | 0.96 |
| 40_L | 43_A | 1.167 | 0.96 |
| 89_A | 93_N | 1.167 | 0.96 |
| 443_L | 446_T | 1.165 | 0.96 |
| 70_L | 74_V | 1.163 | 0.96 |
| 345_R | 348_E | 1.162 | 0.96 |
| 83_S | 87_S | 1.156 | 0.96 |
| 52_L | 55_S | 1.153 | 0.96 |
| 30_Y | 36_R | 1.152 | 0.96 |
| 31_V | 36_R | 1.150 | 0.96 |
| 438_S | 441_T | 1.149 | 0.96 |
| 61_Y | 68_V | 1.146 | 0.95 |
| 451_D | 455_I | 1.145 | 0.95 |
| 38_Y | 43_A | 1.144 | 0.95 |
| 63_T | 68_V | 1.142 | 0.95 |
| 430_S | 434_V | 1.140 | 0.95 |
| 414_P | 419_S | 1.137 | 0.95 |
| 431_L | 435_D | 1.135 | 0.95 |
| 17_G | 20_T | 1.132 | 0.95 |
| 67_A | 70_L | 1.130 | 0.95 |
| 196_R | 200_E | 1.129 | 0.95 |
| 83_S | 93_N | 1.122 | 0.95 |
| 149_L | 153_E | 1.120 | 0.95 |
| 38_Y | 44_L | 1.118 | 0.95 |
| 67_A | 71_R | 1.115 | 0.94 |
| 51_S | 54_A | 1.114 | 0.94 |
| 90_D | 93_N | 1.113 | 0.94 |
| 203_L | 206_F | 1.112 | 0.94 |
| 40_L | 45_R | 1.108 | 0.94 |
| 63_T | 66_S | 1.105 | 0.94 |
| 422_N | 425_E | 1.101 | 0.94 |
| 35_T | 43_A | 1.101 | 0.94 |
| 81_Q | 93_N | 1.100 | 0.94 |
| 34_S | 37_T | 1.098 | 0.94 |
| 72_S | 75_P | 1.098 | 0.94 |
| 84_V | 90_D | 1.097 | 0.94 |
| 68_V | 75_P | 1.095 | 0.94 |
| 307_D | 310_R | 1.088 | 0.94 |
| 74_V | 77_V | 1.087 | 0.93 |
| 125_E | 128_N | 1.077 | 0.93 |
| 214_S | 221_E | 1.077 | 0.93 |
| 36_R | 40_L | 1.077 | 0.93 |
| 58_G | 62_A | 1.076 | 0.93 |
| 64_R | 70_L | 1.076 | 0.93 |
| 132_L | 136_E | 1.074 | 0.93 |
| 211_D | 221_E | 1.074 | 0.93 |
| 80_L | 91_A | 1.069 | 0.93 |
| 440_R | 443_L | 1.067 | 0.93 |
| 401_R | 405_E | 1.067 | 0.93 |
| 61_Y | 65_S | 1.066 | 0.93 |
| 292_K | 296_A | 1.065 | 0.93 |
| 425_E | 429_D | 1.062 | 0.92 |
| 75_P | 78_R | 1.061 | 0.92 |
| 52_L | 57_P | 1.061 | 0.92 |
| 33_T | 40_L | 1.060 | 0.92 |
| 281_A | 284_L | 1.059 | 0.92 |
| 87_S | 93_N | 1.059 | 0.92 |
| 80_L | 87_S | 1.058 | 0.92 |
| 444_I | 447_V | 1.058 | 0.92 |
| 64_R | 67_A | 1.056 | 0.92 |
| 447_V | 450_R | 1.056 | 0.92 |
| 29_S | 36_R | 1.055 | 0.92 |
| 38_Y | 45_R | 1.055 | 0.92 |
| 33_T | 41_G | 1.054 | 0.92 |
| 437_H | 445_K | 1.052 | 0.92 |
| 84_V | 93_N | 1.052 | 0.92 |
| 424_R | 427_N | 1.051 | 0.92 |
| 83_S | 89_A | 1.050 | 0.92 |
| 22_S | 25_S | 1.048 | 0.92 |
| 185_L | 188_K | 1.046 | 0.92 |
| 35_T | 38_Y | 1.045 | 0.92 |
| 80_L | 83_S | 1.040 | 0.91 |
| 85_D | 90_D | 1.038 | 0.91 |
| 32_T | 38_Y | 1.037 | 0.91 |
| 211_D | 225_E | 1.036 | 0.91 |
| 85_D | 92_I | 1.035 | 0.91 |
| 77_V | 87_S | 1.034 | 0.91 |
| 24_P | 32_T | 1.034 | 0.91 |
| 233_F | 241_E | 1.033 | 0.91 |
| 51_S | 56_S | 1.031 | 0.91 |
| 23_R | 34_S | 1.031 | 0.91 |
| 432_P | 435_D | 1.029 | 0.91 |
| 40_L | 47_S | 1.027 | 0.91 |
| 78_R | 82_D | 1.026 | 0.91 |
| 428_L | 431_L | 1.025 | 0.91 |
| 44_L | 52_L | 1.025 | 0.91 |
| 42_S | 48_T | 1.024 | 0.90 |
| 79_L | 85_D | 1.021 | 0.90 |
| 42_S | 46_P | 1.018 | 0.90 |
| 45_R | 53_Y | 1.018 | 0.90 |
| 26_S | 29_S | 1.018 | 0.90 |
| 74_V | 79_L | 1.016 | 0.90 |
| 436_T | 439_K | 1.016 | 0.90 |
| 43_A | 46_P | 1.014 | 0.90 |
| 37_T | 42_S | 1.014 | 0.90 |
| 439_K | 443_L | 1.013 | 0.90 |
| 245_L | 248_Q | 1.013 | 0.90 |
| 64_R | 72_S | 1.013 | 0.90 |
| 436_T | 440_R | 1.010 | 0.90 |
| 437_H | 442_L | 1.010 | 0.90 |
| 214_S | 225_E | 1.009 | 0.90 |
| 49_S | 56_S | 1.009 | 0.90 |
| 79_L | 84_V | 1.009 | 0.90 |
| 302_A | 305_N | 1.008 | 0.90 |
| 452_G | 456_N | 1.006 | 0.89 |
| 82_D | 90_D | 1.006 | 0.89 |
| 239_E | 243_Q | 1.006 | 0.89 |
| 28_R | 38_Y | 1.005 | 0.89 |
| 36_R | 42_S | 1.004 | 0.89 |
| 81_Q | 89_A | 1.003 | 0.89 |
| 412_S | 417_N | 1.002 | 0.89 |
| 35_T | 40_L | 1.002 | 0.89 |
| 43_A | 47_S | 1.002 | 0.89 |
| 34_S | 50_R | 1.001 | 0.89 |
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 | |
| 1deqA | 4 | 0.3112 | 100 | 0.682 | Contact Map |
| 3ghgA | 4 | 0.3476 | 100 | 0.694 | Contact Map |
| 3tnuA | 1 | 0.1931 | 100 | 0.702 | Contact Map |
| 3tnuB | 1 | 0.2039 | 100 | 0.702 | Contact Map |
| 3s4rA | 2 | 0.1953 | 99.9 | 0.765 | Contact Map |
| 3uf1A | 4 | 0.2425 | 99.9 | 0.781 | Contact Map |
| 1gk4A | 6 | 0.1717 | 99.9 | 0.789 | Contact Map |
| 1x8yA | 1 | 0.1588 | 99.8 | 0.801 | Contact Map |
| 3tyyA | 2 | 0.1609 | 99.8 | 0.803 | Contact Map |
| 2xv5A | 2 | 0.1223 | 99.8 | 0.821 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)