| luxA |
| ID: | 1503564511 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 360 (356) | ||
| Sequences: | 14681 (6947.1) | ||
| Seq/Len: | 41.239 | ||
| Nf(neff/√len): | 368.2 |
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: 41.239).
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 |
| 236_S | 306_E | 6.080 | 1.00 |
| 29_R | 65_A | 3.605 | 1.00 |
| 147_D | 152_K | 3.460 | 1.00 |
| 236_S | 303_T | 3.154 | 1.00 |
| 30_I | 33_E | 2.766 | 1.00 |
| 310_I | 313_K | 2.709 | 1.00 |
| 303_T | 306_E | 2.707 | 1.00 |
| 129_E | 185_Q | 2.681 | 1.00 |
| 32_E | 68_K | 2.678 | 1.00 |
| 70_N | 102_R | 2.673 | 1.00 |
| 59_A | 71_V | 2.625 | 1.00 |
| 305_Q | 350_F | 2.610 | 1.00 |
| 126_A | 149_E | 2.609 | 1.00 |
| 30_I | 341_K | 2.587 | 1.00 |
| 312_Q | 316_D | 2.575 | 1.00 |
| 180_T | 207_L | 2.514 | 1.00 |
| 343_F | 347_V | 2.504 | 1.00 |
| 235_D | 238_K | 2.470 | 1.00 |
| 236_S | 240_K | 2.416 | 1.00 |
| 350_F | 353_E | 2.394 | 1.00 |
| 181_E | 211_V | 2.380 | 1.00 |
| 206_E | 210_E | 2.341 | 1.00 |
| 34_C | 344_Q | 2.276 | 1.00 |
| 184_A | 211_V | 2.258 | 1.00 |
| 233_D | 238_K | 2.254 | 1.00 |
| 63_L | 97_S | 2.250 | 1.00 |
| 25_V | 29_R | 2.241 | 1.00 |
| 207_L | 211_V | 2.189 | 1.00 |
| 234_H | 346_D | 2.187 | 1.00 |
| 341_K | 345_S | 2.186 | 1.00 |
| 308_I | 350_F | 2.159 | 1.00 |
| 29_R | 33_E | 2.115 | 1.00 |
| 202_K | 206_E | 2.074 | 1.00 |
| 25_V | 65_A | 2.052 | 1.00 |
| 90_V | 101_F | 1.983 | 1.00 |
| 28_G | 62_L | 1.961 | 1.00 |
| 210_E | 214_E | 1.957 | 1.00 |
| 237_I | 241_E | 1.946 | 1.00 |
| 205_L | 209_N | 1.933 | 1.00 |
| 26_K | 29_R | 1.923 | 1.00 |
| 123_N | 149_E | 1.922 | 1.00 |
| 63_L | 71_V | 1.911 | 1.00 |
| 54_N | 89_D | 1.900 | 1.00 |
| 111_N | 115_R | 1.897 | 1.00 |
| 40_W | 72_G | 1.896 | 1.00 |
| 136_K | 186_F | 1.892 | 1.00 |
| 218_D | 221_N | 1.885 | 1.00 |
| 94_D | 99_G | 1.862 | 1.00 |
| 313_K | 317_A | 1.848 | 1.00 |
| 181_E | 214_E | 1.846 | 1.00 |
| 35_G | 352_K | 1.845 | 1.00 |
| 22_K | 98_K | 1.842 | 1.00 |
| 30_I | 34_C | 1.823 | 1.00 |
| 62_L | 71_V | 1.790 | 1.00 |
| 212_A | 222_I | 1.780 | 1.00 |
| 300_P | 307_C | 1.749 | 1.00 |
| 126_A | 150_H | 1.735 | 1.00 |
| 120_D | 123_N | 1.720 | 1.00 |
| 28_G | 39_V | 1.719 | 1.00 |
| 39_V | 69_L | 1.717 | 1.00 |
| 130_C | 148_N | 1.712 | 1.00 |
| 133_G | 146_A | 1.706 | 1.00 |
| 305_Q | 309_D | 1.675 | 1.00 |
| 16_S | 19_E | 1.653 | 1.00 |
| 133_G | 186_F | 1.628 | 1.00 |
| 306_E | 309_D | 1.623 | 1.00 |
| 136_K | 167_G | 1.618 | 1.00 |
| 137_N | 144_M | 1.605 | 1.00 |
| 342_L | 346_D | 1.595 | 1.00 |
| 90_V | 103_F | 1.586 | 1.00 |
| 174_A | 190_M | 1.580 | 1.00 |
| 2_K | 37_D | 1.566 | 1.00 |
| 32_E | 66_T | 1.558 | 1.00 |
| 181_E | 185_Q | 1.554 | 1.00 |
| 32_E | 67_K | 1.552 | 1.00 |
| 41_L | 59_A | 1.510 | 1.00 |
| 61_Y | 64_G | 1.477 | 1.00 |
| 115_R | 154_H | 1.470 | 1.00 |
| 312_Q | 356_R | 1.464 | 1.00 |
| 145_E | 155_K | 1.459 | 1.00 |
| 28_G | 66_T | 1.449 | 1.00 |
| 18_T | 22_K | 1.440 | 1.00 |
| 306_E | 310_I | 1.437 | 1.00 |
| 226_L | 320_I | 1.433 | 1.00 |
| 238_K | 242_I | 1.426 | 1.00 |
| 202_K | 317_A | 1.408 | 1.00 |
| 203_A | 206_E | 1.401 | 0.99 |
| 61_Y | 96_M | 1.385 | 0.99 |
| 312_Q | 354_K | 1.381 | 0.99 |
| 133_G | 137_N | 1.381 | 0.99 |
| 181_E | 215_Y | 1.380 | 0.99 |
| 33_E | 67_K | 1.380 | 0.99 |
| 5_N | 31_S | 1.378 | 0.99 |
| 25_V | 61_Y | 1.369 | 0.99 |
| 22_K | 26_K | 1.368 | 0.99 |
| 145_E | 154_H | 1.363 | 0.99 |
| 207_L | 210_E | 1.358 | 0.99 |
| 309_D | 313_K | 1.357 | 0.99 |
| 238_K | 241_E | 1.356 | 0.99 |
| 140_T | 167_G | 1.355 | 0.99 |
| 348_M | 352_K | 1.354 | 0.99 |
| 41_L | 62_L | 1.353 | 0.99 |
| 81_A | 89_D | 1.350 | 0.99 |
| 4_G | 38_T | 1.344 | 0.99 |
| 72_G | 102_R | 1.338 | 0.99 |
| 19_E | 23_R | 1.321 | 0.99 |
| 184_A | 215_Y | 1.319 | 0.99 |
| 244_R | 248_G | 1.314 | 0.99 |
| 137_N | 146_A | 1.295 | 0.99 |
| 123_N | 126_A | 1.294 | 0.99 |
| 308_I | 312_Q | 1.288 | 0.99 |
| 86_Q | 131_W | 1.282 | 0.99 |
| 312_Q | 315_I | 1.278 | 0.99 |
| 129_E | 186_F | 1.272 | 0.99 |
| 134_L | 146_A | 1.268 | 0.99 |
| 76_I | 86_Q | 1.265 | 0.99 |
| 350_F | 354_K | 1.261 | 0.99 |
| 56_Y | 76_I | 1.259 | 0.99 |
| 59_A | 73_T | 1.251 | 0.99 |
| 316_D | 356_R | 1.249 | 0.99 |
| 54_N | 57_V | 1.249 | 0.99 |
| 147_D | 154_H | 1.242 | 0.98 |
| 346_D | 350_F | 1.239 | 0.98 |
| 243_C | 247_L | 1.230 | 0.98 |
| 129_E | 133_G | 1.221 | 0.98 |
| 26_K | 30_I | 1.220 | 0.98 |
| 177_A | 207_L | 1.219 | 0.98 |
| 98_K | 163_Y | 1.211 | 0.98 |
| 234_H | 238_K | 1.208 | 0.98 |
| 241_E | 244_R | 1.208 | 0.98 |
| 132_Y | 186_F | 1.201 | 0.98 |
| 171_Y | 189_P | 1.201 | 0.98 |
| 126_A | 178_S | 1.199 | 0.98 |
| 232_V | 307_C | 1.198 | 0.98 |
| 123_N | 150_H | 1.197 | 0.98 |
| 181_E | 207_L | 1.192 | 0.98 |
| 338_A | 342_L | 1.189 | 0.98 |
| 241_E | 245_K | 1.188 | 0.98 |
| 53_G | 92_L | 1.187 | 0.98 |
| 242_I | 342_L | 1.185 | 0.98 |
| 243_C | 301_V | 1.183 | 0.98 |
| 308_I | 347_V | 1.183 | 0.98 |
| 26_K | 337_I | 1.179 | 0.98 |
| 33_E | 345_S | 1.178 | 0.98 |
| 130_C | 149_E | 1.177 | 0.98 |
| 211_V | 214_E | 1.176 | 0.98 |
| 338_A | 341_K | 1.174 | 0.98 |
| 105_I | 132_Y | 1.170 | 0.97 |
| 61_Y | 65_A | 1.169 | 0.97 |
| 94_D | 164_S | 1.160 | 0.97 |
| 139_M | 170_V | 1.160 | 0.97 |
| 93_L | 101_F | 1.151 | 0.97 |
| 309_D | 354_K | 1.147 | 0.97 |
| 56_Y | 89_D | 1.147 | 0.97 |
| 63_L | 101_F | 1.132 | 0.97 |
| 185_Q | 215_Y | 1.119 | 0.96 |
| 134_L | 153_F | 1.116 | 0.96 |
| 103_F | 135_I | 1.115 | 0.96 |
| 212_A | 217_H | 1.111 | 0.96 |
| 57_V | 60_A | 1.108 | 0.96 |
| 131_W | 135_I | 1.107 | 0.96 |
| 200_E | 203_A | 1.089 | 0.96 |
| 228_Y | 311_I | 1.081 | 0.95 |
| 182_W | 186_F | 1.080 | 0.95 |
| 38_T | 72_G | 1.079 | 0.95 |
| 136_K | 188_L | 1.069 | 0.95 |
| 302_G | 307_C | 1.068 | 0.95 |
| 340_M | 344_Q | 1.061 | 0.95 |
| 178_S | 181_E | 1.059 | 0.95 |
| 75_A | 173_V | 1.056 | 0.95 |
| 22_K | 25_V | 1.049 | 0.94 |
| 29_R | 67_K | 1.047 | 0.94 |
| 232_V | 304_P | 1.047 | 0.94 |
| 304_P | 342_L | 1.043 | 0.94 |
| 21_M | 61_Y | 1.043 | 0.94 |
| 135_I | 139_M | 1.041 | 0.94 |
| 28_G | 69_L | 1.038 | 0.94 |
| 137_N | 141_E | 1.036 | 0.94 |
| 235_D | 239_A | 1.030 | 0.94 |
| 37_D | 352_K | 1.028 | 0.94 |
| 309_D | 312_Q | 1.021 | 0.93 |
| 85_R | 89_D | 1.021 | 0.93 |
| 78_L | 86_Q | 1.021 | 0.93 |
| 11_Q | 17_Q | 1.013 | 0.93 |
| 33_E | 341_K | 1.012 | 0.93 |
| 172_V | 183_A | 1.003 | 0.93 |
| 30_I | 337_I | 1.003 | 0.93 |
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 | |
| 1lucA | 1 | 0.9056 | 100 | 0.126 | Contact Map |
| 1lucB | 1 | 0.8889 | 100 | 0.167 | Contact Map |
| 2wgkA | 2 | 0.9556 | 100 | 0.174 | Contact Map |
| 2i7gA | 2 | 0.9278 | 100 | 0.185 | Contact Map |
| 1ezwA | 1 | 0.9028 | 100 | 0.213 | Contact Map |
| 3c8nA | 4 | 0.8944 | 100 | 0.215 | Contact Map |
| 3raoA | 2 | 0.9278 | 100 | 0.216 | Contact Map |
| 1rhcA | 1 | 0.8861 | 100 | 0.221 | Contact Map |
| 1z69A | 4 | 0.8889 | 100 | 0.225 | Contact Map |
| 3b9oA | 2 | 0.9556 | 100 | 0.235 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)