| dradnramp |
| ID: | 1405515858 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 436 (405) | ||
| Sequences: | 1877 (1268) | ||
| Seq/Len: | 4.635 | ||
| Nf(neff/√len): | 63.0 |
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: 4.635).
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 |
| 101_R | 109_E | 5.693 | 1.00 |
| 200_D | 203_A | 4.095 | 1.00 |
| 397_A | 412_T | 2.933 | 1.00 |
| 110_R | 398_R | 2.633 | 1.00 |
| 396_T | 407_T | 2.540 | 1.00 |
| 407_T | 412_T | 2.382 | 1.00 |
| 409_R | 413_V | 2.322 | 1.00 |
| 302_Q | 305_T | 2.302 | 1.00 |
| 393_L | 415_G | 2.268 | 1.00 |
| 98_A | 405_L | 2.236 | 1.00 |
| 399_R | 406_V | 2.200 | 1.00 |
| 390_V | 423_I | 2.173 | 1.00 |
| 90_N | 94_N | 2.056 | 1.00 |
| 87_V | 418_I | 1.927 | 1.00 |
| 208_F | 276_M | 1.901 | 1.00 |
| 142_I | 146_T | 1.851 | 1.00 |
| 397_A | 407_T | 1.782 | 1.00 |
| 409_R | 412_T | 1.769 | 1.00 |
| 201_L | 204_V | 1.765 | 1.00 |
| 420_V | 424_A | 1.699 | 0.99 |
| 352_R | 356_T | 1.697 | 0.99 |
| 332_T | 336_D | 1.685 | 0.99 |
| 84_M | 418_I | 1.670 | 0.99 |
| 101_R | 106_L | 1.664 | 0.99 |
| 233_V | 330_V | 1.653 | 0.99 |
| 48_V | 267_A | 1.646 | 0.99 |
| 112_P | 115_L | 1.642 | 0.99 |
| 91_L | 407_T | 1.637 | 0.99 |
| 94_N | 407_T | 1.626 | 0.99 |
| 61_A | 300_A | 1.625 | 0.99 |
| 204_V | 280_A | 1.615 | 0.99 |
| 90_N | 261_R | 1.613 | 0.99 |
| 428_Y | 432_E | 1.612 | 0.99 |
| 427_G | 431_W | 1.611 | 0.99 |
| 299_T | 302_Q | 1.608 | 0.99 |
| 99_S | 401_V | 1.606 | 0.99 |
| 197_A | 284_A | 1.594 | 0.99 |
| 173_R | 177_L | 1.589 | 0.99 |
| 54_Y | 271_A | 1.588 | 0.99 |
| 111_W | 394_L | 1.582 | 0.99 |
| 239_A | 337_V | 1.581 | 0.99 |
| 102_N | 105_E | 1.578 | 0.99 |
| 65_E | 69_R | 1.559 | 0.99 |
| 40_I | 262_V | 1.556 | 0.99 |
| 183_V | 326_S | 1.535 | 0.99 |
| 95_L | 106_L | 1.523 | 0.98 |
| 86_M | 265_I | 1.522 | 0.98 |
| 106_L | 109_E | 1.511 | 0.98 |
| 141_A | 321_L | 1.489 | 0.98 |
| 114_P | 118_F | 1.482 | 0.98 |
| 276_M | 280_A | 1.480 | 0.98 |
| 389_L | 419_A | 1.459 | 0.98 |
| 390_V | 419_A | 1.455 | 0.98 |
| 390_V | 394_L | 1.451 | 0.98 |
| 93_A | 260_N | 1.440 | 0.98 |
| 62_T | 223_G | 1.440 | 0.98 |
| 305_T | 313_S | 1.413 | 0.97 |
| 398_R | 401_V | 1.408 | 0.97 |
| 130_T | 134_E | 1.407 | 0.97 |
| 95_L | 396_T | 1.404 | 0.97 |
| 148_L | 156_V | 1.381 | 0.97 |
| 219_Y | 376_L | 1.378 | 0.97 |
| 133_A | 377_S | 1.372 | 0.96 |
| 70_Y | 216_G | 1.364 | 0.96 |
| 193_Q | 281_V | 1.361 | 0.96 |
| 194_V | 280_A | 1.358 | 0.96 |
| 88_I | 389_L | 1.337 | 0.96 |
| 57_P | 324_G | 1.332 | 0.96 |
| 117_W | 121_I | 1.311 | 0.95 |
| 59_N | 63_N | 1.305 | 0.95 |
| 50_A | 264_V | 1.286 | 0.94 |
| 184_L | 188_V | 1.285 | 0.94 |
| 269_G | 273_L | 1.284 | 0.94 |
| 395_F | 401_V | 1.279 | 0.94 |
| 39_R | 255_R | 1.278 | 0.94 |
| 75_L | 276_M | 1.277 | 0.94 |
| 411_F | 415_G | 1.273 | 0.94 |
| 148_L | 153_G | 1.273 | 0.94 |
| 270_L | 274_I | 1.271 | 0.94 |
| 348_P | 351_L | 1.263 | 0.94 |
| 351_L | 355_I | 1.258 | 0.93 |
| 52_I | 56_D | 1.252 | 0.93 |
| 227_A | 230_M | 1.243 | 0.93 |
| 393_L | 397_A | 1.242 | 0.93 |
| 305_T | 310_P | 1.239 | 0.93 |
| 374_L | 377_S | 1.238 | 0.93 |
| 394_L | 398_R | 1.237 | 0.93 |
| 84_M | 225_I | 1.234 | 0.93 |
| 200_D | 204_V | 1.221 | 0.92 |
| 60_F | 319_A | 1.220 | 0.92 |
| 155_V | 159_V | 1.220 | 0.92 |
| 49_I | 330_V | 1.219 | 0.92 |
| 108_R | 116_V | 1.203 | 0.91 |
| 424_A | 427_G | 1.202 | 0.91 |
| 89_Q | 104_P | 1.201 | 0.91 |
| 133_A | 374_L | 1.200 | 0.91 |
| 54_Y | 59_N | 1.199 | 0.91 |
| 63_N | 275_N | 1.195 | 0.91 |
| 282_A | 285_T | 1.191 | 0.91 |
| 56_D | 59_N | 1.188 | 0.91 |
| 53_A | 60_F | 1.183 | 0.90 |
| 394_L | 416_W | 1.182 | 0.90 |
| 157_T | 321_L | 1.181 | 0.90 |
| 94_N | 323_S | 1.177 | 0.90 |
| 47_A | 51_S | 1.174 | 0.90 |
| 186_I | 327_S | 1.172 | 0.90 |
| 351_L | 354_L | 1.167 | 0.90 |
| 423_I | 427_G | 1.166 | 0.90 |
| 63_N | 278_M | 1.160 | 0.89 |
| 107_I | 119_Y | 1.156 | 0.89 |
| 137_G | 320_L | 1.154 | 0.89 |
| 130_T | 133_A | 1.154 | 0.89 |
| 369_D | 372_S | 1.153 | 0.89 |
| 219_Y | 379_V | 1.151 | 0.89 |
| 194_V | 277_S | 1.143 | 0.88 |
| 263_D | 267_A | 1.140 | 0.88 |
| 87_V | 411_F | 1.129 | 0.87 |
| 91_L | 95_L | 1.126 | 0.87 |
| 300_A | 320_L | 1.125 | 0.87 |
| 233_V | 237_H | 1.120 | 0.87 |
| 45_G | 263_D | 1.117 | 0.87 |
| 72_Y | 284_A | 1.116 | 0.87 |
| 53_A | 330_V | 1.113 | 0.86 |
| 421_I | 424_A | 1.105 | 0.86 |
| 61_A | 374_L | 1.100 | 0.86 |
| 121_I | 125_L | 1.093 | 0.85 |
| 156_V | 159_V | 1.091 | 0.85 |
| 306_P | 312_A | 1.090 | 0.85 |
| 379_V | 392_L | 1.087 | 0.85 |
| 130_T | 381_L | 1.086 | 0.85 |
| 202_A | 206_A | 1.085 | 0.84 |
| 333_M | 337_V | 1.085 | 0.84 |
| 51_S | 55_M | 1.081 | 0.84 |
| 398_R | 406_V | 1.079 | 0.84 |
| 258_R | 262_V | 1.078 | 0.84 |
| 69_R | 216_G | 1.078 | 0.84 |
| 408_R | 411_F | 1.078 | 0.84 |
| 412_T | 416_W | 1.076 | 0.84 |
| 406_V | 409_R | 1.069 | 0.83 |
| 191_L | 277_S | 1.069 | 0.83 |
| 143_Q | 298_T | 1.065 | 0.83 |
| 120_W | 124_E | 1.064 | 0.83 |
| 228_T | 378_Q | 1.055 | 0.82 |
| 56_D | 130_T | 1.054 | 0.82 |
| 376_L | 380_I | 1.053 | 0.82 |
| 134_E | 137_G | 1.052 | 0.82 |
| 99_S | 106_L | 1.052 | 0.82 |
| 54_Y | 232_H | 1.049 | 0.82 |
| 203_A | 206_A | 1.048 | 0.82 |
| 416_W | 420_V | 1.046 | 0.81 |
| 190_Y | 207_G | 1.045 | 0.81 |
| 59_N | 275_N | 1.045 | 0.81 |
| 301_Y | 313_S | 1.043 | 0.81 |
| 134_E | 227_A | 1.042 | 0.81 |
| 56_D | 134_E | 1.035 | 0.80 |
| 224_I | 279_L | 1.034 | 0.80 |
| 134_E | 377_S | 1.033 | 0.80 |
| 413_V | 424_A | 1.031 | 0.80 |
| 331_G | 339_M | 1.028 | 0.80 |
| 158_G | 370_P | 1.027 | 0.80 |
| 311_A | 315_L | 1.026 | 0.80 |
| 417_V | 430_L | 1.025 | 0.80 |
| 231_P | 234_I | 1.025 | 0.80 |
| 70_Y | 214_G | 1.024 | 0.79 |
| 172_T | 243_G | 1.024 | 0.79 |
| 78_I | 285_T | 1.022 | 0.79 |
| 233_V | 236_L | 1.021 | 0.79 |
| 62_T | 278_M | 1.021 | 0.79 |
| 232_H | 238_S | 1.020 | 0.79 |
| 419_A | 423_I | 1.020 | 0.79 |
| 217_S | 393_L | 1.019 | 0.79 |
| 327_S | 331_G | 1.019 | 0.79 |
| 47_A | 141_A | 1.015 | 0.79 |
| 59_N | 230_M | 1.015 | 0.79 |
| 231_P | 381_L | 1.014 | 0.78 |
| 149_P | 152_W | 1.011 | 0.78 |
| 330_V | 384_G | 1.009 | 0.78 |
| 196_L | 427_G | 1.009 | 0.78 |
| 53_A | 388_A | 1.007 | 0.78 |
| 109_E | 158_G | 1.006 | 0.78 |
| 192_V | 196_L | 1.004 | 0.78 |
| 206_A | 211_R | 1.002 | 0.77 |
| 358_L | 361_F | 1.001 | 0.77 |
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 | |
| 2jlnA | 1 | 0.9151 | 99.2 | 0.871 | Contact Map |
| 3dh4A | 4 | 0.8509 | 99 | 0.884 | Contact Map |
| 2xq2A | 1 | 0.8991 | 98.7 | 0.894 | Contact Map |
| 3giaA | 1 | 0.8555 | 98.6 | 0.899 | Contact Map |
| 3l1lA | 1 | 0.8372 | 98.6 | 0.899 | Contact Map |
| 4djkA | 2 | 0.8326 | 98.4 | 0.903 | Contact Map |
| 2a65A | 1 | 0.8693 | 96.2 | 0.935 | Contact Map |
| 4m48A | 1 | 0.8624 | 93.2 | 0.945 | Contact Map |
| 4eneA | 2 | 0.5894 | 3.4 | 0.98 | Contact Map |
| 1zrxA | 1 | 0.0963 | 2.8 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)