| LarC |
| ID: | 1446058201 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 420 (407) | ||
| Sequences: | 736 (620.6) | ||
| Seq/Len: | 1.808 | ||
| Nf(neff/√len): | 30.8 |
HHblits Results: (2015_06)
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: 1.808).
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 |
| 116_I | 219_L | 3.050 | 1.00 |
| 372_Q | 390_D | 2.921 | 1.00 |
| 57_G | 243_F | 2.774 | 1.00 |
| 101_D | 114_K | 2.774 | 1.00 |
| 106_S | 157_E | 2.592 | 1.00 |
| 363_T | 370_D | 2.582 | 1.00 |
| 125_A | 132_L | 2.531 | 1.00 |
| 292_G | 316_D | 2.498 | 1.00 |
| 6_L | 17_F | 2.494 | 1.00 |
| 18_L | 151_G | 2.473 | 1.00 |
| 294_V | 342_T | 2.443 | 1.00 |
| 345_I | 376_A | 2.401 | 1.00 |
| 371_V | 394_L | 2.309 | 1.00 |
| 233_N | 259_F | 2.264 | 1.00 |
| 292_G | 318_P | 2.216 | 0.99 |
| 322_L | 338_I | 2.213 | 0.99 |
| 237_T | 260_E | 2.211 | 0.99 |
| 365_A | 370_D | 2.170 | 0.99 |
| 31_L | 155_G | 2.164 | 0.99 |
| 187_V | 190_V | 2.157 | 0.99 |
| 18_L | 60_F | 2.109 | 0.99 |
| 34_E | 37_K | 2.088 | 0.99 |
| 24_L | 258_L | 2.085 | 0.99 |
| 6_L | 256_A | 1.996 | 0.99 |
| 295_M | 306_V | 1.976 | 0.99 |
| 126_A | 192_Q | 1.938 | 0.98 |
| 27_D | 158_L | 1.888 | 0.98 |
| 169_L | 212_I | 1.883 | 0.98 |
| 293_Y | 341_E | 1.862 | 0.98 |
| 15_D | 59_S | 1.850 | 0.98 |
| 50_E | 243_F | 1.848 | 0.97 |
| 366_T | 369_G | 1.837 | 0.97 |
| 171_D | 201_I | 1.833 | 0.97 |
| 389_A | 392_A | 1.820 | 0.97 |
| 120_I | 193_M | 1.808 | 0.97 |
| 17_F | 152_C | 1.807 | 0.97 |
| 327_N | 330_D | 1.801 | 0.97 |
| 191_M | 257_V | 1.792 | 0.97 |
| 330_D | 333_L | 1.779 | 0.97 |
| 59_S | 245_K | 1.777 | 0.97 |
| 307_F | 323_T | 1.760 | 0.96 |
| 119_E | 221_K | 1.759 | 0.96 |
| 192_Q | 195_V | 1.746 | 0.96 |
| 20_A | 256_A | 1.736 | 0.96 |
| 274_D | 356_I | 1.704 | 0.95 |
| 121_A | 132_L | 1.687 | 0.95 |
| 93_L | 97_E | 1.683 | 0.95 |
| 52_Q | 247_D | 1.683 | 0.95 |
| 49_R | 56_Y | 1.652 | 0.94 |
| 394_L | 398_F | 1.642 | 0.94 |
| 97_E | 114_K | 1.623 | 0.94 |
| 17_F | 219_L | 1.618 | 0.93 |
| 26_L | 155_G | 1.617 | 0.93 |
| 279_I | 349_Y | 1.599 | 0.93 |
| 309_T | 323_T | 1.597 | 0.93 |
| 290_G | 406_Y | 1.588 | 0.93 |
| 163_T | 226_E | 1.574 | 0.92 |
| 283_L | 322_L | 1.560 | 0.92 |
| 287_T | 291_L | 1.557 | 0.92 |
| 30_Q | 158_L | 1.556 | 0.92 |
| 112_H | 157_E | 1.545 | 0.91 |
| 12_I | 17_F | 1.540 | 0.91 |
| 156_L | 164_I | 1.539 | 0.91 |
| 311_I | 319_A | 1.539 | 0.91 |
| 48_Q | 61_D | 1.513 | 0.90 |
| 311_I | 321_K | 1.503 | 0.90 |
| 119_E | 222_T | 1.490 | 0.89 |
| 277_L | 331_K | 1.482 | 0.89 |
| 118_M | 122_Q | 1.476 | 0.89 |
| 119_E | 193_M | 1.475 | 0.88 |
| 291_L | 308_F | 1.472 | 0.88 |
| 335_T | 339_L | 1.436 | 0.87 |
| 19_G | 59_S | 1.436 | 0.87 |
| 97_E | 118_M | 1.434 | 0.87 |
| 57_G | 253_A | 1.433 | 0.86 |
| 50_E | 57_G | 1.422 | 0.86 |
| 276_V | 354_R | 1.409 | 0.85 |
| 4_L | 24_L | 1.404 | 0.85 |
| 278_M | 323_T | 1.382 | 0.84 |
| 367_P | 412_A | 1.380 | 0.84 |
| 169_L | 220_V | 1.372 | 0.83 |
| 200_P | 227_F | 1.353 | 0.82 |
| 212_I | 217_M | 1.352 | 0.82 |
| 173_S | 208_H | 1.348 | 0.82 |
| 393_Q | 397_Q | 1.348 | 0.82 |
| 286_Q | 343_T | 1.330 | 0.80 |
| 47_Q | 60_F | 1.330 | 0.80 |
| 361_F | 372_Q | 1.329 | 0.80 |
| 166_A | 220_V | 1.316 | 0.79 |
| 46_T | 63_Q | 1.316 | 0.79 |
| 92_H | 95_D | 1.312 | 0.79 |
| 12_I | 212_I | 1.305 | 0.79 |
| 190_V | 217_M | 1.304 | 0.79 |
| 209_T | 246_R | 1.304 | 0.79 |
| 26_L | 158_L | 1.303 | 0.78 |
| 408_A | 412_A | 1.299 | 0.78 |
| 331_K | 349_Y | 1.291 | 0.78 |
| 279_I | 347_V | 1.289 | 0.77 |
| 35_L | 43_Y | 1.281 | 0.77 |
| 312_Q | 316_D | 1.279 | 0.77 |
| 4_L | 256_A | 1.278 | 0.77 |
| 146_I | 150_V | 1.269 | 0.76 |
| 282_N | 323_T | 1.269 | 0.76 |
| 276_V | 352_W | 1.249 | 0.74 |
| 175_F | 182_Q | 1.236 | 0.73 |
| 400_I | 408_A | 1.235 | 0.73 |
| 78_H | 81_E | 1.233 | 0.73 |
| 278_M | 350_Q | 1.231 | 0.73 |
| 100_I | 110_K | 1.230 | 0.73 |
| 336_K | 340_Q | 1.229 | 0.72 |
| 391_C | 402_F | 1.228 | 0.72 |
| 163_T | 225_R | 1.223 | 0.72 |
| 283_L | 286_Q | 1.221 | 0.72 |
| 116_I | 223_L | 1.220 | 0.72 |
| 275_A | 351_T | 1.215 | 0.71 |
| 62_V | 147_V | 1.215 | 0.71 |
| 143_L | 147_V | 1.212 | 0.71 |
| 8_A | 167_S | 1.208 | 0.71 |
| 383_K | 403_R | 1.202 | 0.70 |
| 161_I | 258_L | 1.201 | 0.70 |
| 295_M | 308_F | 1.197 | 0.70 |
| 340_Q | 380_D | 1.194 | 0.69 |
| 289_E | 385_M | 1.171 | 0.67 |
| 112_H | 153_C | 1.168 | 0.67 |
| 307_F | 311_I | 1.163 | 0.66 |
| 326_G | 334_L | 1.161 | 0.66 |
| 127_V | 192_Q | 1.153 | 0.65 |
| 335_T | 349_Y | 1.152 | 0.65 |
| 116_I | 153_C | 1.147 | 0.65 |
| 335_T | 355_T | 1.138 | 0.64 |
| 339_L | 357_M | 1.137 | 0.64 |
| 5_Y | 167_S | 1.134 | 0.64 |
| 195_V | 239_V | 1.134 | 0.64 |
| 294_V | 322_L | 1.132 | 0.63 |
| 13_S | 19_G | 1.129 | 0.63 |
| 404_T | 407_Q | 1.127 | 0.63 |
| 155_G | 256_A | 1.123 | 0.62 |
| 6_L | 219_L | 1.118 | 0.62 |
| 177_N | 182_Q | 1.116 | 0.62 |
| 364_V | 409_A | 1.113 | 0.61 |
| 108_T | 157_E | 1.111 | 0.61 |
| 334_L | 337_L | 1.098 | 0.60 |
| 72_F | 77_H | 1.096 | 0.60 |
| 153_C | 219_L | 1.095 | 0.60 |
| 293_Y | 388_Y | 1.093 | 0.59 |
| 288_G | 294_V | 1.091 | 0.59 |
| 106_S | 154_I | 1.089 | 0.59 |
| 98_A | 102_G | 1.087 | 0.59 |
| 392_A | 396_Q | 1.085 | 0.58 |
| 276_V | 304_Y | 1.084 | 0.58 |
| 297_Q | 341_E | 1.081 | 0.58 |
| 122_Q | 274_D | 1.079 | 0.58 |
| 74_E | 77_H | 1.076 | 0.58 |
| 144_D | 148_D | 1.069 | 0.57 |
| 71_G | 74_E | 1.067 | 0.57 |
| 109_V | 157_E | 1.063 | 0.56 |
| 107_D | 111_H | 1.062 | 0.56 |
| 80_H | 83_G | 1.061 | 0.56 |
| 303_A | 334_L | 1.061 | 0.56 |
| 407_Q | 410_L | 1.060 | 0.56 |
| 360_H | 377_T | 1.058 | 0.56 |
| 71_G | 76_H | 1.058 | 0.56 |
| 121_A | 137_F | 1.054 | 0.55 |
| 287_T | 290_G | 1.052 | 0.55 |
| 299_L | 305_D | 1.052 | 0.55 |
| 34_E | 154_I | 1.046 | 0.54 |
| 391_C | 406_Y | 1.043 | 0.54 |
| 79_Q | 82_A | 1.043 | 0.54 |
| 56_Y | 129_H | 1.039 | 0.54 |
| 144_D | 180_H | 1.038 | 0.53 |
| 4_L | 164_I | 1.037 | 0.53 |
| 22_L | 47_Q | 1.033 | 0.53 |
| 73_V | 77_H | 1.032 | 0.53 |
| 45_L | 96_I | 1.031 | 0.53 |
| 282_N | 307_F | 1.030 | 0.53 |
| 145_S | 153_C | 1.028 | 0.52 |
| 343_T | 357_M | 1.026 | 0.52 |
| 13_S | 254_L | 1.025 | 0.52 |
| 3_T | 165_M | 1.021 | 0.52 |
| 391_C | 405_V | 1.019 | 0.51 |
| 260_E | 329_N | 1.018 | 0.51 |
| 8_A | 100_I | 1.016 | 0.51 |
| 124_E | 138_H | 1.015 | 0.51 |
| 91_R | 117_F | 1.014 | 0.51 |
| 279_I | 331_K | 1.013 | 0.51 |
| 371_V | 409_A | 1.011 | 0.51 |
| 354_R | 359_R | 1.009 | 0.50 |
| 124_E | 215_T | 1.007 | 0.50 |
| 281_A | 347_V | 1.006 | 0.50 |
| 73_V | 76_H | 1.005 | 0.50 |
| 125_A | 131_P | 1.002 | 0.50 |
| 313_M | 319_A | 1.002 | 0.50 |
| 100_I | 150_V | 1.002 | 0.50 |
| 117_F | 146_I | 1.001 | 0.49 |
| 288_G | 292_G | 1.001 | 0.49 |
| 130_M | 134_E | 1.000 | 0.49 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3c19A | 1 | 0.3643 | 100 | 0.67 | Contact Map |
| 3tutA | 1 | 0.631 | 85.7 | 0.968 | Contact Map |
| 3vu1A | 2 | 0.1786 | 80.6 | 0.97 | Contact Map |
| 1jr2A | 2 | 0.5024 | 75 | 0.971 | Contact Map |
| 3kzhA | 2 | 0.1667 | 63.1 | 0.973 | Contact Map |
| 4nnzA | 2 | 0.1524 | 62.7 | 0.973 | Contact Map |
| 3ie7A | 1 | 0.1548 | 61.4 | 0.974 | Contact Map |
| 4hjzA | 2 | 0.4095 | 56.8 | 0.974 | Contact Map |
| 3ljsA | 2 | 0.1476 | 52.9 | 0.975 | Contact Map |
| 3ewmA | 2 | 0.1619 | 50.5 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)