| LarC |
| ID: | 1494573413 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 420 (409) | ||
| Sequences: | 823 (666.9) | ||
| Seq/Len: | 2.012 | ||
| Nf(neff/√len): | 33.0 |
HHblits Results: (2016_02)
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: 2.012).
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 | 3.348 | 1.00 |
| 372_Q | 390_D | 3.326 | 1.00 |
| 57_G | 243_F | 3.275 | 1.00 |
| 101_D | 114_K | 3.127 | 1.00 |
| 363_T | 370_D | 2.810 | 1.00 |
| 294_V | 342_T | 2.771 | 1.00 |
| 106_S | 157_E | 2.748 | 1.00 |
| 6_L | 17_F | 2.632 | 1.00 |
| 125_A | 132_L | 2.612 | 1.00 |
| 18_L | 151_G | 2.545 | 1.00 |
| 322_L | 338_I | 2.534 | 1.00 |
| 371_V | 394_L | 2.516 | 1.00 |
| 237_T | 260_E | 2.457 | 1.00 |
| 18_L | 60_F | 2.441 | 1.00 |
| 292_G | 316_D | 2.331 | 1.00 |
| 393_Q | 397_Q | 2.312 | 1.00 |
| 295_M | 306_V | 2.207 | 1.00 |
| 292_G | 318_P | 2.205 | 1.00 |
| 24_L | 258_L | 2.202 | 1.00 |
| 234_A | 259_F | 2.195 | 1.00 |
| 34_E | 37_K | 2.137 | 0.99 |
| 17_F | 152_C | 2.089 | 0.99 |
| 169_L | 212_I | 2.081 | 0.99 |
| 31_L | 155_G | 2.067 | 0.99 |
| 6_L | 256_A | 2.051 | 0.99 |
| 50_E | 243_F | 2.035 | 0.99 |
| 187_V | 190_V | 2.033 | 0.99 |
| 394_L | 398_F | 2.004 | 0.99 |
| 59_S | 245_K | 1.981 | 0.99 |
| 121_A | 132_L | 1.960 | 0.99 |
| 126_A | 192_Q | 1.956 | 0.99 |
| 26_L | 155_G | 1.924 | 0.99 |
| 97_E | 114_K | 1.917 | 0.99 |
| 120_I | 193_M | 1.917 | 0.99 |
| 330_D | 333_L | 1.894 | 0.98 |
| 12_I | 17_F | 1.890 | 0.98 |
| 327_N | 330_D | 1.887 | 0.98 |
| 93_L | 97_E | 1.887 | 0.98 |
| 15_D | 59_S | 1.868 | 0.98 |
| 163_T | 226_E | 1.854 | 0.98 |
| 293_Y | 341_E | 1.851 | 0.98 |
| 192_Q | 195_V | 1.832 | 0.98 |
| 276_V | 354_R | 1.819 | 0.98 |
| 389_A | 392_A | 1.809 | 0.98 |
| 191_M | 257_V | 1.790 | 0.97 |
| 307_F | 323_T | 1.789 | 0.97 |
| 274_D | 356_I | 1.784 | 0.97 |
| 57_G | 253_A | 1.776 | 0.97 |
| 119_E | 221_K | 1.750 | 0.97 |
| 171_D | 201_I | 1.715 | 0.96 |
| 283_L | 322_L | 1.708 | 0.96 |
| 309_T | 323_T | 1.705 | 0.96 |
| 50_E | 57_G | 1.652 | 0.95 |
| 279_I | 349_Y | 1.636 | 0.95 |
| 287_T | 291_L | 1.616 | 0.95 |
| 28_F | 32_K | 1.610 | 0.94 |
| 200_P | 227_F | 1.600 | 0.94 |
| 4_L | 24_L | 1.599 | 0.94 |
| 112_H | 157_E | 1.594 | 0.94 |
| 311_I | 319_A | 1.593 | 0.94 |
| 17_F | 219_L | 1.571 | 0.93 |
| 20_A | 256_A | 1.569 | 0.93 |
| 49_R | 56_Y | 1.547 | 0.93 |
| 52_Q | 247_D | 1.539 | 0.92 |
| 277_L | 331_K | 1.527 | 0.92 |
| 291_L | 308_F | 1.512 | 0.92 |
| 119_E | 222_T | 1.492 | 0.91 |
| 116_I | 153_C | 1.472 | 0.90 |
| 8_A | 167_S | 1.464 | 0.90 |
| 331_K | 349_Y | 1.438 | 0.89 |
| 118_M | 122_Q | 1.435 | 0.89 |
| 278_M | 323_T | 1.429 | 0.88 |
| 286_Q | 343_T | 1.428 | 0.88 |
| 295_M | 308_F | 1.427 | 0.88 |
| 312_Q | 316_D | 1.424 | 0.88 |
| 311_I | 321_K | 1.422 | 0.88 |
| 4_L | 256_A | 1.404 | 0.87 |
| 335_T | 355_T | 1.397 | 0.87 |
| 155_G | 256_A | 1.386 | 0.86 |
| 48_Q | 61_D | 1.384 | 0.86 |
| 335_T | 349_Y | 1.378 | 0.86 |
| 335_T | 339_L | 1.377 | 0.86 |
| 156_L | 164_I | 1.376 | 0.86 |
| 326_G | 334_L | 1.371 | 0.85 |
| 275_A | 351_T | 1.371 | 0.85 |
| 97_E | 118_M | 1.367 | 0.85 |
| 383_K | 403_R | 1.358 | 0.85 |
| 166_A | 220_V | 1.325 | 0.83 |
| 161_I | 258_L | 1.317 | 0.82 |
| 282_N | 323_T | 1.314 | 0.82 |
| 276_V | 352_W | 1.312 | 0.82 |
| 5_Y | 167_S | 1.311 | 0.82 |
| 35_L | 43_Y | 1.308 | 0.81 |
| 283_L | 286_Q | 1.296 | 0.81 |
| 175_F | 182_Q | 1.294 | 0.80 |
| 146_I | 150_V | 1.293 | 0.80 |
| 109_V | 113_A | 1.291 | 0.80 |
| 92_H | 95_D | 1.272 | 0.79 |
| 19_G | 59_S | 1.266 | 0.78 |
| 212_I | 217_M | 1.266 | 0.78 |
| 163_T | 225_R | 1.265 | 0.78 |
| 169_L | 220_V | 1.261 | 0.78 |
| 278_M | 352_W | 1.261 | 0.78 |
| 279_I | 347_V | 1.260 | 0.78 |
| 354_R | 359_R | 1.259 | 0.78 |
| 190_V | 217_M | 1.258 | 0.78 |
| 392_A | 396_Q | 1.253 | 0.77 |
| 3_T | 165_M | 1.249 | 0.77 |
| 361_F | 372_Q | 1.244 | 0.77 |
| 366_T | 369_G | 1.237 | 0.76 |
| 289_E | 385_M | 1.233 | 0.76 |
| 107_D | 111_H | 1.233 | 0.76 |
| 394_L | 400_I | 1.232 | 0.76 |
| 288_G | 294_V | 1.229 | 0.75 |
| 276_V | 304_Y | 1.224 | 0.75 |
| 119_E | 193_M | 1.208 | 0.74 |
| 62_V | 147_V | 1.204 | 0.73 |
| 127_V | 192_Q | 1.202 | 0.73 |
| 121_A | 137_F | 1.201 | 0.73 |
| 12_I | 212_I | 1.177 | 0.71 |
| 391_C | 402_F | 1.174 | 0.71 |
| 23_D | 240_G | 1.166 | 0.70 |
| 106_S | 154_I | 1.165 | 0.70 |
| 334_L | 337_L | 1.160 | 0.69 |
| 178_V | 183_M | 1.159 | 0.69 |
| 315_K | 389_A | 1.155 | 0.69 |
| 100_I | 110_K | 1.150 | 0.68 |
| 299_L | 306_V | 1.144 | 0.68 |
| 339_L | 357_M | 1.144 | 0.68 |
| 112_H | 153_C | 1.143 | 0.68 |
| 336_K | 340_Q | 1.134 | 0.67 |
| 44_E | 63_Q | 1.132 | 0.67 |
| 303_A | 334_L | 1.126 | 0.66 |
| 34_E | 154_I | 1.126 | 0.66 |
| 30_Q | 158_L | 1.120 | 0.65 |
| 409_A | 412_A | 1.120 | 0.65 |
| 307_F | 311_I | 1.120 | 0.65 |
| 297_Q | 341_E | 1.118 | 0.65 |
| 109_V | 157_E | 1.117 | 0.65 |
| 177_N | 182_Q | 1.117 | 0.65 |
| 304_Y | 354_R | 1.114 | 0.65 |
| 365_A | 369_G | 1.110 | 0.64 |
| 278_M | 350_Q | 1.109 | 0.64 |
| 209_T | 246_R | 1.108 | 0.64 |
| 143_L | 147_V | 1.108 | 0.64 |
| 339_L | 347_V | 1.107 | 0.64 |
| 289_E | 383_K | 1.105 | 0.64 |
| 363_T | 372_Q | 1.098 | 0.63 |
| 287_T | 292_G | 1.098 | 0.63 |
| 125_A | 131_P | 1.098 | 0.63 |
| 46_T | 63_Q | 1.098 | 0.63 |
| 117_F | 145_S | 1.095 | 0.63 |
| 103_S | 110_K | 1.092 | 0.63 |
| 43_Y | 147_V | 1.092 | 0.63 |
| 105_L | 109_V | 1.092 | 0.63 |
| 153_C | 219_L | 1.090 | 0.62 |
| 303_A | 313_M | 1.089 | 0.62 |
| 288_G | 292_G | 1.089 | 0.62 |
| 209_T | 248_T | 1.087 | 0.62 |
| 137_F | 140_V | 1.085 | 0.62 |
| 117_F | 142_A | 1.083 | 0.62 |
| 282_N | 307_F | 1.081 | 0.61 |
| 294_V | 322_L | 1.081 | 0.61 |
| 195_V | 239_V | 1.080 | 0.61 |
| 103_S | 145_S | 1.077 | 0.61 |
| 293_Y | 388_Y | 1.076 | 0.61 |
| 108_T | 157_E | 1.076 | 0.61 |
| 243_F | 253_A | 1.075 | 0.61 |
| 93_L | 114_K | 1.068 | 0.60 |
| 119_E | 122_Q | 1.061 | 0.59 |
| 282_N | 321_K | 1.055 | 0.59 |
| 11_G | 14_G | 1.054 | 0.58 |
| 276_V | 325_L | 1.052 | 0.58 |
| 144_D | 148_D | 1.047 | 0.58 |
| 287_T | 290_G | 1.045 | 0.57 |
| 176_I | 183_M | 1.045 | 0.57 |
| 144_D | 180_H | 1.044 | 0.57 |
| 145_S | 153_C | 1.044 | 0.57 |
| 55_I | 241_Y | 1.043 | 0.57 |
| 308_F | 316_D | 1.043 | 0.57 |
| 274_D | 354_R | 1.042 | 0.57 |
| 4_L | 164_I | 1.039 | 0.57 |
| 282_N | 305_D | 1.037 | 0.57 |
| 26_L | 158_L | 1.035 | 0.56 |
| 116_I | 223_L | 1.030 | 0.56 |
| 343_T | 357_M | 1.030 | 0.56 |
| 47_Q | 58_T | 1.028 | 0.56 |
| 23_D | 49_R | 1.026 | 0.55 |
| 22_L | 31_L | 1.020 | 0.55 |
| 408_A | 412_A | 1.018 | 0.54 |
| 161_I | 164_I | 1.017 | 0.54 |
| 5_Y | 165_M | 1.016 | 0.54 |
| 307_F | 325_L | 1.016 | 0.54 |
| 190_V | 194_R | 1.014 | 0.54 |
| 22_L | 28_F | 1.013 | 0.54 |
| 166_A | 227_F | 1.012 | 0.54 |
| 10_S | 388_Y | 1.012 | 0.54 |
| 124_E | 215_T | 1.010 | 0.54 |
| 13_S | 254_L | 1.010 | 0.54 |
| 313_M | 319_A | 1.007 | 0.53 |
| 13_S | 19_G | 1.004 | 0.53 |
| 324_V | 334_L | 1.003 | 0.53 |
| 32_K | 36_A | 1.002 | 0.53 |
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 | |
| 3c19A | 1 | 0.369 | 100 | 0.671 | Contact Map |
| 3vu1A | 2 | 0.1833 | 76.9 | 0.97 | Contact Map |
| 3tutA | 1 | 0.6262 | 74.9 | 0.97 | Contact Map |
| 3mc9A | 2 | 0.0048 | 51.2 | 0.975 | Contact Map |
| 4usiA | 3 | 0.2286 | 51 | 0.975 | Contact Map |
| 1q1oA | 1 | 0.119 | 48.6 | 0.975 | Contact Map |
| 3kzhA | 2 | 0.1738 | 46 | 0.975 | Contact Map |
| 3ewmA | 2 | 0.1619 | 45 | 0.976 | Contact Map |
| 1jr2A | 2 | 0.5333 | 44.5 | 0.976 | Contact Map |
| 3ie7A | 1 | 0.15 | 35.3 | 0.977 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)