| arsM for coevolution analysis |
| ID: | 1485874386 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 375 (354) | ||
| Sequences: | 386 (246.3) | ||
| Seq/Len: | 1.090 | ||
| Nf(neff/√len): | 13.1 |
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: 1.090).
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 |
| 105_K | 133_H | 4.591 | 1.00 |
| 278_G | 318_D | 3.040 | 1.00 |
| 170_E | 173_R | 2.783 | 1.00 |
| 192_L | 250_C | 2.698 | 1.00 |
| 146_N | 173_R | 2.693 | 1.00 |
| 196_I | 208_G | 2.370 | 0.99 |
| 30_N | 237_T | 2.328 | 0.99 |
| 146_N | 170_E | 2.269 | 0.99 |
| 294_F | 300_V | 2.216 | 0.98 |
| 170_E | 174_V | 2.188 | 0.98 |
| 152_V | 171_A | 2.125 | 0.98 |
| 73_W | 99_T | 2.097 | 0.97 |
| 165_Q | 222_K | 2.047 | 0.97 |
| 292_F | 303_D | 2.020 | 0.96 |
| 240_N | 244_E | 2.007 | 0.96 |
| 99_T | 149_H | 1.961 | 0.96 |
| 85_C | 115_L | 1.951 | 0.95 |
| 19_Q | 106_G | 1.922 | 0.95 |
| 10_Q | 13_V | 1.892 | 0.94 |
| 49_N | 90_Q | 1.880 | 0.94 |
| 51_H | 118_H | 1.874 | 0.94 |
| 72_C | 151_I | 1.861 | 0.94 |
| 199_H | 246_V | 1.858 | 0.94 |
| 206_C | 252_F | 1.824 | 0.93 |
| 28_Q | 240_N | 1.793 | 0.92 |
| 138_K | 141_E | 1.762 | 0.91 |
| 186_V | 206_C | 1.749 | 0.91 |
| 97_H | 130_T | 1.746 | 0.91 |
| 112_E | 115_L | 1.739 | 0.90 |
| 230_L | 255_A | 1.694 | 0.89 |
| 158_I | 167_V | 1.689 | 0.89 |
| 50_V | 87_V | 1.664 | 0.88 |
| 119_M | 127_S | 1.639 | 0.86 |
| 58_Y | 64_V | 1.626 | 0.86 |
| 88_L | 153_V | 1.621 | 0.86 |
| 30_N | 240_N | 1.615 | 0.85 |
| 11_K | 14_Q | 1.598 | 0.84 |
| 73_W | 149_H | 1.590 | 0.84 |
| 73_W | 97_H | 1.549 | 0.82 |
| 187_Y | 228_P | 1.497 | 0.79 |
| 79_S | 85_C | 1.491 | 0.78 |
| 153_V | 199_H | 1.488 | 0.78 |
| 43_I | 46_A | 1.481 | 0.78 |
| 186_V | 252_F | 1.478 | 0.78 |
| 49_N | 121_K | 1.449 | 0.76 |
| 54_V | 86_Y | 1.421 | 0.74 |
| 21_L | 27_L | 1.415 | 0.73 |
| 46_A | 50_V | 1.410 | 0.73 |
| 40_P | 207_L | 1.399 | 0.72 |
| 194_E | 198_T | 1.387 | 0.71 |
| 49_N | 89_S | 1.381 | 0.70 |
| 218_V | 269_K | 1.370 | 0.70 |
| 192_L | 199_H | 1.355 | 0.68 |
| 278_G | 283_E | 1.351 | 0.68 |
| 15_T | 19_Q | 1.348 | 0.68 |
| 237_T | 244_E | 1.347 | 0.68 |
| 39_V | 43_I | 1.324 | 0.66 |
| 172_Y | 261_K | 1.319 | 0.65 |
| 75_L | 149_H | 1.314 | 0.65 |
| 237_T | 240_N | 1.306 | 0.64 |
| 59_Y | 206_C | 1.305 | 0.64 |
| 197_R | 208_G | 1.295 | 0.63 |
| 118_H | 122_Y | 1.288 | 0.63 |
| 302_V | 306_T | 1.287 | 0.63 |
| 41_K | 46_A | 1.281 | 0.62 |
| 186_V | 236_I | 1.281 | 0.62 |
| 271_C | 303_D | 1.269 | 0.61 |
| 115_L | 119_M | 1.268 | 0.61 |
| 295_K | 298_E | 1.261 | 0.60 |
| 220_A | 259_L | 1.261 | 0.60 |
| 213_W | 255_A | 1.260 | 0.60 |
| 135_Y | 161_V | 1.256 | 0.60 |
| 159_N | 206_C | 1.255 | 0.60 |
| 51_H | 117_Y | 1.255 | 0.60 |
| 348_K | 351_E | 1.250 | 0.59 |
| 273_V | 299_I | 1.235 | 0.58 |
| 272_Q | 322_R | 1.235 | 0.58 |
| 30_N | 244_E | 1.231 | 0.57 |
| 44_R | 203_W | 1.221 | 0.57 |
| 192_L | 208_G | 1.220 | 0.56 |
| 228_P | 259_L | 1.195 | 0.54 |
| 214_K | 218_V | 1.190 | 0.54 |
| 233_A | 290_A | 1.189 | 0.54 |
| 272_Q | 323_P | 1.185 | 0.53 |
| 345_D | 348_K | 1.175 | 0.52 |
| 193_P | 250_C | 1.173 | 0.52 |
| 286_L | 314_R | 1.172 | 0.52 |
| 116_D | 296_E | 1.170 | 0.52 |
| 188_T | 192_L | 1.166 | 0.51 |
| 177_H | 284_K | 1.161 | 0.51 |
| 88_L | 118_H | 1.160 | 0.51 |
| 168_L | 259_L | 1.160 | 0.51 |
| 18_G | 27_L | 1.154 | 0.50 |
| 14_Q | 135_Y | 1.152 | 0.50 |
| 192_L | 195_E | 1.148 | 0.50 |
| 345_D | 350_A | 1.145 | 0.49 |
| 271_C | 333_G | 1.141 | 0.49 |
| 132_I | 163_D | 1.137 | 0.49 |
| 165_Q | 219_L | 1.136 | 0.49 |
| 217_A | 223_I | 1.136 | 0.49 |
| 116_D | 119_M | 1.135 | 0.48 |
| 124_F | 247_I | 1.134 | 0.48 |
| 54_V | 118_H | 1.134 | 0.48 |
| 276_N | 320_L | 1.134 | 0.48 |
| 303_D | 328_L | 1.128 | 0.48 |
| 42_H | 281_G | 1.124 | 0.47 |
| 107_Q | 159_N | 1.119 | 0.47 |
| 52_E | 101_I | 1.114 | 0.46 |
| 225_F | 228_P | 1.098 | 0.45 |
| 146_N | 174_V | 1.097 | 0.45 |
| 46_A | 90_Q | 1.089 | 0.44 |
| 30_N | 236_I | 1.087 | 0.44 |
| 208_G | 250_C | 1.084 | 0.44 |
| 303_D | 306_T | 1.083 | 0.44 |
| 144_I | 174_V | 1.080 | 0.43 |
| 217_A | 269_K | 1.077 | 0.43 |
| 310_L | 321_I | 1.076 | 0.43 |
| 18_G | 21_L | 1.072 | 0.42 |
| 44_R | 296_E | 1.069 | 0.42 |
| 344_T | 353_S | 1.066 | 0.42 |
| 349_L | 352_E | 1.064 | 0.42 |
| 270_R | 333_G | 1.063 | 0.42 |
| 75_L | 174_V | 1.062 | 0.42 |
| 192_L | 197_R | 1.060 | 0.41 |
| 235_L | 240_N | 1.060 | 0.41 |
| 51_H | 314_R | 1.057 | 0.41 |
| 70_E | 95_K | 1.056 | 0.41 |
| 15_T | 20_V | 1.053 | 0.41 |
| 21_L | 24_S | 1.048 | 0.40 |
| 89_S | 129_V | 1.047 | 0.40 |
| 98_V | 215_E | 1.047 | 0.40 |
| 171_A | 196_I | 1.047 | 0.40 |
| 165_Q | 169_Q | 1.047 | 0.40 |
| 285_E | 293_T | 1.045 | 0.40 |
| 338_E | 344_T | 1.040 | 0.40 |
| 124_F | 128_N | 1.038 | 0.39 |
| 191_E | 212_Y | 1.035 | 0.39 |
| 108_V | 217_A | 1.032 | 0.39 |
| 13_V | 103_M | 1.027 | 0.38 |
| 281_G | 297_G | 1.027 | 0.38 |
| 118_H | 129_V | 1.024 | 0.38 |
| 92_V | 128_N | 1.024 | 0.38 |
| 194_E | 242_E | 1.021 | 0.38 |
| 136_I | 161_V | 1.019 | 0.38 |
| 344_T | 350_A | 1.017 | 0.37 |
| 210_A | 252_F | 1.013 | 0.37 |
| 51_H | 122_Y | 1.013 | 0.37 |
| 271_C | 306_T | 1.012 | 0.37 |
| 214_K | 217_A | 1.012 | 0.37 |
| 101_I | 165_Q | 1.008 | 0.37 |
| 60_G | 102_D | 1.008 | 0.37 |
| 18_G | 104_T | 1.007 | 0.37 |
| 21_L | 26_D | 1.007 | 0.37 |
| 67_E | 315_F | 1.006 | 0.37 |
| 274_I | 299_I | 1.006 | 0.37 |
| 42_H | 46_A | 1.004 | 0.36 |
| 104_T | 167_V | 1.004 | 0.36 |
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 | |
| 4fsdA | 1 | 0.8267 | 100 | 0.652 | Contact Map |
| 4obxA | 4 | 0.5573 | 99.9 | 0.847 | Contact Map |
| 4krgA | 2 | 0.6107 | 99.9 | 0.848 | Contact Map |
| 3l8dA | 1 | 0.5307 | 99.9 | 0.85 | Contact Map |
| 4p7cA | 2 | 0.7093 | 99.9 | 0.851 | Contact Map |
| 3busA | 2 | 0.6507 | 99.9 | 0.852 | Contact Map |
| 3ujcA | 1 | 0.648 | 99.9 | 0.853 | Contact Map |
| 2o57A | 4 | 0.7173 | 99.9 | 0.853 | Contact Map |
| 3g5lA | 2 | 0.5307 | 99.9 | 0.854 | Contact Map |
| 4pneA | 2 | 0.712 | 99.9 | 0.854 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)