| LPH |
| ID: | 1446049118 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 451 (351) | ||
| Sequences: | 1367 (838.1) | ||
| Seq/Len: | 3.895 | ||
| Nf(neff/√len): | 44.7 |
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: 3.895).
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 |
| 205_H | 221_D | 3.462 | 1.00 |
| 270_C | 281_C | 3.447 | 1.00 |
| 149_Y | 175_T | 3.341 | 1.00 |
| 263_C | 327_C | 2.987 | 1.00 |
| 232_G | 250_R | 2.945 | 1.00 |
| 75_V | 160_S | 2.925 | 1.00 |
| 203_V | 218_G | 2.811 | 1.00 |
| 175_T | 202_D | 2.618 | 1.00 |
| 66_N | 69_K | 2.534 | 1.00 |
| 149_Y | 173_R | 2.467 | 1.00 |
| 173_R | 202_D | 2.441 | 1.00 |
| 69_K | 100_D | 2.432 | 1.00 |
| 128_A | 132_K | 2.421 | 1.00 |
| 150_M | 160_S | 2.359 | 1.00 |
| 164_G | 174_I | 2.261 | 1.00 |
| 143_A | 148_I | 2.129 | 1.00 |
| 203_V | 221_D | 2.127 | 1.00 |
| 128_A | 162_F | 2.002 | 1.00 |
| 149_Y | 202_D | 1.972 | 1.00 |
| 284_C | 292_C | 1.862 | 1.00 |
| 193_L | 203_V | 1.825 | 1.00 |
| 216_P | 223_Y | 1.812 | 1.00 |
| 91_L | 256_L | 1.802 | 0.99 |
| 120_A | 123_K | 1.800 | 0.99 |
| 151_I | 177_L | 1.800 | 0.99 |
| 128_A | 163_V | 1.797 | 0.99 |
| 124_T | 159_I | 1.741 | 0.99 |
| 111_G | 123_K | 1.718 | 0.99 |
| 161_G | 164_G | 1.715 | 0.99 |
| 65_L | 71_T | 1.706 | 0.99 |
| 60_S | 63_G | 1.704 | 0.99 |
| 48_R | 100_D | 1.698 | 0.99 |
| 176_G | 193_L | 1.691 | 0.99 |
| 108_W | 112_A | 1.641 | 0.99 |
| 47_T | 50_N | 1.620 | 0.99 |
| 70_K | 147_D | 1.619 | 0.99 |
| 224_P | 318_F | 1.594 | 0.98 |
| 174_I | 193_L | 1.594 | 0.98 |
| 321_A | 328_M | 1.570 | 0.98 |
| 213_Y | 217_L | 1.554 | 0.98 |
| 175_T | 200_F | 1.533 | 0.98 |
| 320_T | 325_P | 1.512 | 0.98 |
| 200_F | 299_A | 1.474 | 0.97 |
| 320_T | 326_F | 1.467 | 0.97 |
| 73_F | 135_I | 1.454 | 0.97 |
| 295_L | 318_F | 1.452 | 0.97 |
| 153_V | 251_S | 1.448 | 0.97 |
| 154_S | 180_A | 1.447 | 0.97 |
| 75_V | 131_L | 1.427 | 0.96 |
| 95_L | 297_Y | 1.426 | 0.96 |
| 146_D | 199_Q | 1.421 | 0.96 |
| 257_S | 265_I | 1.401 | 0.96 |
| 131_L | 163_V | 1.398 | 0.96 |
| 157_A | 176_G | 1.386 | 0.95 |
| 132_K | 166_M | 1.385 | 0.95 |
| 225_N | 231_P | 1.380 | 0.95 |
| 173_R | 200_F | 1.377 | 0.95 |
| 149_Y | 200_F | 1.373 | 0.95 |
| 123_K | 126_K | 1.364 | 0.95 |
| 71_T | 102_N | 1.363 | 0.95 |
| 200_F | 220_I | 1.354 | 0.95 |
| 203_V | 217_L | 1.341 | 0.94 |
| 121_S | 124_T | 1.334 | 0.94 |
| 176_G | 203_V | 1.322 | 0.94 |
| 150_M | 163_V | 1.315 | 0.93 |
| 204_I | 295_L | 1.298 | 0.93 |
| 144_S | 147_D | 1.293 | 0.93 |
| 78_F | 120_A | 1.288 | 0.92 |
| 129_M | 166_M | 1.282 | 0.92 |
| 65_L | 102_N | 1.275 | 0.92 |
| 76_H | 108_W | 1.275 | 0.92 |
| 201_V | 205_H | 1.271 | 0.92 |
| 72_T | 151_I | 1.267 | 0.92 |
| 94_G | 260_R | 1.263 | 0.91 |
| 250_R | 257_S | 1.260 | 0.91 |
| 204_I | 224_P | 1.252 | 0.91 |
| 255_Y | 258_S | 1.247 | 0.91 |
| 181_G | 213_Y | 1.246 | 0.91 |
| 145_L | 172_G | 1.233 | 0.90 |
| 198_A | 201_V | 1.227 | 0.90 |
| 71_T | 104_V | 1.222 | 0.90 |
| 208_T | 214_K | 1.218 | 0.89 |
| 273_Y | 277_R | 1.209 | 0.89 |
| 249_Q | 252_V | 1.209 | 0.89 |
| 265_I | 295_L | 1.207 | 0.89 |
| 270_C | 279_G | 1.196 | 0.88 |
| 150_M | 171_L | 1.191 | 0.88 |
| 72_T | 175_T | 1.179 | 0.87 |
| 216_P | 315_K | 1.162 | 0.86 |
| 202_D | 299_A | 1.158 | 0.86 |
| 158_H | 192_R | 1.153 | 0.86 |
| 272_S | 275_D | 1.151 | 0.85 |
| 96_L | 100_D | 1.143 | 0.85 |
| 245_K | 249_Q | 1.143 | 0.85 |
| 293_P | 312_P | 1.143 | 0.85 |
| 201_V | 221_D | 1.136 | 0.84 |
| 124_T | 162_F | 1.135 | 0.84 |
| 75_V | 150_M | 1.131 | 0.84 |
| 153_V | 252_V | 1.130 | 0.84 |
| 254_L | 257_S | 1.130 | 0.84 |
| 132_K | 163_V | 1.125 | 0.84 |
| 59_S | 63_G | 1.119 | 0.83 |
| 353_D | 387_D | 1.110 | 0.82 |
| 372_K | 376_V | 1.102 | 0.82 |
| 106_V | 131_L | 1.099 | 0.82 |
| 162_F | 165_E | 1.098 | 0.82 |
| 233_C | 246_C | 1.097 | 0.81 |
| 72_T | 173_R | 1.094 | 0.81 |
| 72_T | 149_Y | 1.092 | 0.81 |
| 212_G | 227_G | 1.092 | 0.81 |
| 193_L | 198_A | 1.088 | 0.81 |
| 273_Y | 276_Y | 1.088 | 0.81 |
| 158_H | 163_V | 1.087 | 0.81 |
| 47_T | 64_N | 1.087 | 0.81 |
| 47_T | 55_Q | 1.087 | 0.81 |
| 225_N | 230_Q | 1.080 | 0.80 |
| 393_S | 398_T | 1.080 | 0.80 |
| 43_L | 184_F | 1.078 | 0.80 |
| 55_Q | 63_G | 1.071 | 0.79 |
| 121_S | 182_P | 1.065 | 0.79 |
| 370_F | 374_H | 1.065 | 0.79 |
| 47_T | 63_G | 1.061 | 0.78 |
| 218_G | 223_Y | 1.058 | 0.78 |
| 75_V | 159_I | 1.057 | 0.78 |
| 111_G | 263_C | 1.057 | 0.78 |
| 192_R | 197_D | 1.055 | 0.78 |
| 41_V | 130_V | 1.053 | 0.78 |
| 149_Y | 258_S | 1.052 | 0.78 |
| 82_G | 87_W | 1.051 | 0.77 |
| 39_L | 111_G | 1.051 | 0.77 |
| 193_L | 197_D | 1.050 | 0.77 |
| 276_Y | 279_G | 1.046 | 0.77 |
| 87_W | 91_L | 1.043 | 0.77 |
| 120_A | 155_L | 1.038 | 0.76 |
| 335_I | 392_I | 1.036 | 0.76 |
| 72_T | 101_M | 1.033 | 0.76 |
| 332_F | 338_W | 1.032 | 0.76 |
| 221_D | 232_G | 1.030 | 0.75 |
| 174_I | 197_D | 1.030 | 0.75 |
| 388_K | 393_S | 1.030 | 0.75 |
| 224_P | 254_L | 1.027 | 0.75 |
| 153_V | 160_S | 1.027 | 0.75 |
| 201_V | 218_G | 1.024 | 0.75 |
| 129_M | 191_D | 1.022 | 0.75 |
| 359_T | 362_K | 1.020 | 0.74 |
| 50_N | 64_N | 1.017 | 0.74 |
| 54_A | 57_I | 1.016 | 0.74 |
| 78_F | 121_S | 1.015 | 0.74 |
| 125_R | 191_D | 1.014 | 0.74 |
| 266_T | 294_L | 1.012 | 0.74 |
| 224_P | 295_L | 1.011 | 0.74 |
| 223_Y | 226_G | 1.010 | 0.73 |
| 39_L | 125_R | 1.009 | 0.73 |
| 254_L | 320_T | 1.007 | 0.73 |
| 176_G | 217_L | 1.004 | 0.73 |
| 57_I | 104_V | 1.000 | 0.72 |
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 | |
| 1w52X | 1 | 0.9091 | 100 | 0.345 | Contact Map |
| 1hplA | 2 | 0.9135 | 100 | 0.346 | Contact Map |
| 1rp1A | 1 | 0.8936 | 100 | 0.348 | Contact Map |
| 1bu8A | 1 | 0.9069 | 100 | 0.355 | Contact Map |
| 1gplA | 1 | 0.898 | 100 | 0.375 | Contact Map |
| 4qnnA | 4 | 0 | 100 | 0.541 | Contact Map |
| 1ispA | 1 | 0.3836 | 98.8 | 0.918 | Contact Map |
| 2zshA | 1 | 0.561 | 98.7 | 0.919 | Contact Map |
| 1auoA | 2 | 0.4368 | 98.7 | 0.92 | Contact Map |
| 1uxoA | 1 | 0.3814 | 98.6 | 0.922 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)