| 4pue |
| ID: | 1474534751 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 371 (336) | ||
| Sequences: | 2834 (1964.8) | ||
| Seq/Len: | 8.435 | ||
| Nf(neff/√len): | 107.2 |
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: 8.435).
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 |
| 78_K | 142_D | 3.898 | 1.00 |
| 181_R | 221_D | 3.757 | 1.00 |
| 174_K | 216_E | 3.648 | 1.00 |
| 74_V | 84_I | 3.448 | 1.00 |
| 353_V | 367_I | 3.324 | 1.00 |
| 59_Q | 63_G | 3.288 | 1.00 |
| 61_E | 64_K | 3.196 | 1.00 |
| 355_G | 359_K | 2.923 | 1.00 |
| 161_N | 166_Q | 2.870 | 1.00 |
| 133_K | 137_E | 2.692 | 1.00 |
| 192_M | 206_L | 2.688 | 1.00 |
| 191_Y | 222_G | 2.636 | 1.00 |
| 285_A | 366_A | 2.556 | 1.00 |
| 240_E | 297_K | 2.527 | 1.00 |
| 120_N | 123_L | 2.503 | 1.00 |
| 189_K | 252_D | 2.441 | 1.00 |
| 125_L | 168_A | 2.232 | 1.00 |
| 59_Q | 65_F | 2.076 | 1.00 |
| 125_L | 175_V | 2.068 | 1.00 |
| 71_D | 138_R | 2.058 | 1.00 |
| 255_I | 258_L | 2.038 | 1.00 |
| 121_K | 168_A | 2.024 | 1.00 |
| 55_P | 99_F | 2.017 | 1.00 |
| 244_N | 248_A | 2.006 | 1.00 |
| 129_E | 133_K | 1.990 | 1.00 |
| 71_D | 139_Y | 1.987 | 1.00 |
| 289_D | 366_A | 1.977 | 1.00 |
| 67_F | 134_T | 1.963 | 1.00 |
| 41_K | 80_N | 1.899 | 1.00 |
| 175_V | 178_Q | 1.874 | 1.00 |
| 159_L | 165_Y | 1.863 | 1.00 |
| 141_D | 185_G | 1.860 | 1.00 |
| 152_V | 192_M | 1.846 | 1.00 |
| 289_D | 293_K | 1.830 | 1.00 |
| 154_G | 158_K | 1.827 | 1.00 |
| 254_Q | 303_S | 1.827 | 1.00 |
| 133_K | 179_A | 1.808 | 1.00 |
| 66_N | 69_Q | 1.808 | 1.00 |
| 26_V | 40_L | 1.793 | 1.00 |
| 75_K | 79_A | 1.788 | 1.00 |
| 39_M | 354_F | 1.784 | 1.00 |
| 204_T | 245_M | 1.783 | 1.00 |
| 312_D | 361_K | 1.776 | 1.00 |
| 240_E | 244_N | 1.775 | 1.00 |
| 286_A | 290_R | 1.758 | 1.00 |
| 74_V | 142_D | 1.754 | 1.00 |
| 76_F | 80_N | 1.746 | 1.00 |
| 252_D | 301_K | 1.744 | 1.00 |
| 207_Y | 245_M | 1.709 | 1.00 |
| 85_R | 256_T | 1.692 | 1.00 |
| 11_Q | 14_Q | 1.668 | 1.00 |
| 48_V | 306_T | 1.658 | 1.00 |
| 43_H | 364_Y | 1.649 | 1.00 |
| 133_K | 182_K | 1.645 | 1.00 |
| 62_E | 123_L | 1.639 | 1.00 |
| 292_F | 305_V | 1.638 | 1.00 |
| 129_E | 179_A | 1.636 | 1.00 |
| 121_K | 125_L | 1.611 | 1.00 |
| 75_K | 78_K | 1.592 | 1.00 |
| 24_A | 40_L | 1.580 | 1.00 |
| 119_Q | 127_R | 1.580 | 1.00 |
| 15_R | 368_I | 1.575 | 1.00 |
| 191_Y | 254_Q | 1.572 | 1.00 |
| 59_Q | 130_T | 1.563 | 1.00 |
| 90_V | 128_L | 1.562 | 1.00 |
| 175_V | 179_A | 1.540 | 1.00 |
| 65_F | 130_T | 1.539 | 1.00 |
| 121_K | 171_D | 1.516 | 1.00 |
| 152_V | 173_I | 1.507 | 1.00 |
| 140_K | 185_G | 1.506 | 1.00 |
| 149_V | 152_V | 1.499 | 1.00 |
| 75_K | 142_D | 1.491 | 1.00 |
| 177_F | 220_I | 1.487 | 1.00 |
| 210_V | 251_L | 1.482 | 1.00 |
| 212_Q | 216_E | 1.474 | 1.00 |
| 129_E | 182_K | 1.452 | 0.99 |
| 24_A | 310_I | 1.447 | 0.99 |
| 179_A | 182_K | 1.446 | 0.99 |
| 197_T | 206_L | 1.441 | 0.99 |
| 85_R | 145_Y | 1.433 | 0.99 |
| 92_H | 162_S | 1.431 | 0.99 |
| 247_A | 301_K | 1.423 | 0.99 |
| 244_N | 298_L | 1.418 | 0.99 |
| 67_F | 138_R | 1.415 | 0.99 |
| 181_R | 219_P | 1.415 | 0.99 |
| 295_Y | 302_I | 1.412 | 0.99 |
| 162_S | 172_Y | 1.401 | 0.99 |
| 207_Y | 249_L | 1.395 | 0.99 |
| 252_D | 303_S | 1.383 | 0.99 |
| 211_K | 249_L | 1.378 | 0.99 |
| 55_P | 59_Q | 1.358 | 0.99 |
| 119_Q | 123_L | 1.350 | 0.99 |
| 203_R | 242_T | 1.340 | 0.99 |
| 225_H | 243_I | 1.334 | 0.99 |
| 70_A | 138_R | 1.326 | 0.99 |
| 168_A | 175_V | 1.307 | 0.99 |
| 174_K | 178_Q | 1.297 | 0.98 |
| 86_F | 143_I | 1.294 | 0.98 |
| 46_S | 306_T | 1.288 | 0.98 |
| 83_D | 144_K | 1.287 | 0.98 |
| 321_A | 347_G | 1.286 | 0.98 |
| 288_Y | 363_A | 1.248 | 0.98 |
| 58_I | 135_I | 1.243 | 0.98 |
| 365_W | 369_D | 1.243 | 0.98 |
| 232_G | 287_R | 1.242 | 0.98 |
| 165_Y | 170_I | 1.240 | 0.98 |
| 178_Q | 218_V | 1.222 | 0.97 |
| 210_V | 220_I | 1.218 | 0.97 |
| 74_V | 78_K | 1.217 | 0.97 |
| 13_D | 45_N | 1.215 | 0.97 |
| 261_S | 317_L | 1.212 | 0.97 |
| 245_M | 248_A | 1.193 | 0.97 |
| 204_T | 208_N | 1.185 | 0.97 |
| 313_N | 358_Y | 1.180 | 0.97 |
| 153_V | 209_L | 1.169 | 0.96 |
| 30_Q | 50_E | 1.167 | 0.96 |
| 49_A | 53_M | 1.163 | 0.96 |
| 282_L | 286_A | 1.142 | 0.96 |
| 206_L | 209_L | 1.131 | 0.95 |
| 185_G | 188_I | 1.129 | 0.95 |
| 159_L | 173_I | 1.129 | 0.95 |
| 228_H | 259_D | 1.120 | 0.95 |
| 258_L | 305_V | 1.120 | 0.95 |
| 170_I | 212_Q | 1.105 | 0.95 |
| 311_A | 358_Y | 1.098 | 0.94 |
| 311_A | 314_H | 1.097 | 0.94 |
| 214_K | 249_L | 1.091 | 0.94 |
| 163_P | 167_I | 1.089 | 0.94 |
| 174_K | 212_Q | 1.084 | 0.94 |
| 261_S | 349_D | 1.084 | 0.94 |
| 360_V | 364_Y | 1.084 | 0.94 |
| 43_H | 360_V | 1.083 | 0.94 |
| 197_T | 246_F | 1.079 | 0.94 |
| 143_I | 146_W | 1.079 | 0.94 |
| 210_V | 223_I | 1.077 | 0.94 |
| 27_E | 50_E | 1.076 | 0.94 |
| 47_I | 77_A | 1.076 | 0.94 |
| 37_V | 41_K | 1.070 | 0.93 |
| 214_K | 251_L | 1.070 | 0.93 |
| 85_R | 254_Q | 1.066 | 0.93 |
| 21_T | 304_N | 1.059 | 0.93 |
| 126_K | 130_T | 1.056 | 0.93 |
| 203_R | 245_M | 1.050 | 0.93 |
| 124_L | 167_I | 1.048 | 0.92 |
| 153_V | 206_L | 1.047 | 0.92 |
| 62_E | 127_R | 1.042 | 0.92 |
| 258_L | 291_L | 1.041 | 0.92 |
| 35_K | 38_Q | 1.038 | 0.92 |
| 197_T | 225_H | 1.032 | 0.92 |
| 317_L | 349_D | 1.031 | 0.92 |
| 281_F | 350_A | 1.027 | 0.91 |
| 95_V | 164_W | 1.026 | 0.91 |
| 133_K | 184_G | 1.021 | 0.91 |
| 55_P | 131_H | 1.021 | 0.91 |
| 27_E | 52_V | 1.016 | 0.91 |
| 171_D | 175_V | 1.016 | 0.91 |
| 260_V | 287_R | 1.016 | 0.91 |
| 153_V | 205_A | 1.016 | 0.91 |
| 152_V | 177_F | 1.011 | 0.91 |
| 128_L | 164_W | 1.009 | 0.90 |
| 123_L | 127_R | 1.008 | 0.90 |
| 128_L | 179_A | 1.008 | 0.90 |
| 283_D | 287_R | 1.005 | 0.90 |
| 213_L | 216_E | 1.004 | 0.90 |
| 254_Q | 304_N | 1.000 | 0.90 |
| 59_Q | 131_H | 1.000 | 0.90 |
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 | |
| 1r85A | 1 | 0.9973 | 100 | 0.151 | Contact Map |
| 4qdmA | 2 | 0 | 100 | 0.221 | Contact Map |
| 2w5fA | 2 | 0.8491 | 100 | 0.228 | Contact Map |
| 1us2A | 1 | 0.8976 | 100 | 0.243 | Contact Map |
| 3ro8A | 8 | 0.7682 | 100 | 0.26 | Contact Map |
| 2depA | 2 | 0.9084 | 100 | 0.26 | Contact Map |
| 1ur1A | 1 | 0.8787 | 100 | 0.281 | Contact Map |
| 1w32A | 2 | 0.8464 | 100 | 0.286 | Contact Map |
| 4hu8A | 8 | 0.8787 | 100 | 0.29 | Contact Map |
| 4k68A | 2 | 0.8868 | 100 | 0.297 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)