| VGLUT2 60-520 |
| ID: | 1485160119 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 461 (416) | ||
| Sequences: | 48956 (30100) | ||
| Seq/Len: | 117.683 | ||
| Nf(neff/√len): | 1475.8 |
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: 117.683).
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_V | 120_C | 4.059 | 1.00 |
| 104_S | 194_G | 3.816 | 1.00 |
| 102_L | 131_V | 3.799 | 1.00 |
| 109_L | 124_V | 3.333 | 1.00 |
| 111_P | 188_Y | 3.320 | 1.00 |
| 119_G | 123_F | 3.215 | 1.00 |
| 285_E | 288_K | 3.048 | 1.00 |
| 92_A | 145_K | 2.750 | 1.00 |
| 153_S | 312_D | 2.715 | 1.00 |
| 75_G | 126_I | 2.694 | 1.00 |
| 261_F | 397_S | 2.671 | 1.00 |
| 117_H | 120_C | 2.662 | 1.00 |
| 265_W | 401_C | 2.620 | 1.00 |
| 61_D | 64_T | 2.612 | 1.00 |
| 99_A | 134_V | 2.596 | 1.00 |
| 221_R | 224_E | 2.539 | 1.00 |
| 11_R | 151_E | 2.499 | 1.00 |
| 83_G | 134_V | 2.446 | 1.00 |
| 151_E | 154_R | 2.421 | 1.00 |
| 106_L | 131_V | 2.406 | 1.00 |
| 79_T | 130_L | 2.372 | 1.00 |
| 378_I | 386_L | 2.359 | 1.00 |
| 88_S | 384_S | 2.318 | 1.00 |
| 106_L | 124_V | 2.315 | 1.00 |
| 79_T | 133_G | 2.309 | 1.00 |
| 118_Y | 122_I | 2.281 | 1.00 |
| 246_K | 382_Y | 2.242 | 1.00 |
| 71_S | 126_I | 2.222 | 1.00 |
| 147_A | 155_L | 2.197 | 1.00 |
| 97_G | 198_Y | 2.160 | 1.00 |
| 60_W | 118_Y | 2.145 | 1.00 |
| 113_A | 120_C | 2.130 | 1.00 |
| 108_M | 191_G | 2.064 | 1.00 |
| 106_L | 127_L | 2.034 | 1.00 |
| 245_R | 249_T | 2.032 | 1.00 |
| 181_T | 185_S | 2.023 | 1.00 |
| 101_L | 198_Y | 2.010 | 1.00 |
| 422_L | 426_L | 2.006 | 1.00 |
| 148_P | 151_E | 2.001 | 1.00 |
| 201_W | 205_S | 1.988 | 1.00 |
| 86_I | 95_V | 1.936 | 1.00 |
| 269_L | 405_V | 1.933 | 1.00 |
| 104_S | 198_Y | 1.922 | 1.00 |
| 379_A | 382_Y | 1.843 | 1.00 |
| 177_L | 185_S | 1.841 | 1.00 |
| 97_G | 202_L | 1.820 | 1.00 |
| 93_N | 97_G | 1.815 | 1.00 |
| 84_G | 88_S | 1.782 | 1.00 |
| 199_M | 203_L | 1.776 | 1.00 |
| 85_Y | 89_R | 1.767 | 1.00 |
| 87_A | 138_A | 1.746 | 1.00 |
| 110_I | 121_V | 1.744 | 1.00 |
| 71_S | 122_I | 1.741 | 1.00 |
| 108_M | 112_S | 1.732 | 1.00 |
| 182_G | 185_S | 1.720 | 1.00 |
| 19_G | 162_G | 1.691 | 1.00 |
| 309_Q | 313_F | 1.687 | 1.00 |
| 68_I | 121_V | 1.682 | 1.00 |
| 279_E | 289_V | 1.678 | 1.00 |
| 257_I | 393_V | 1.669 | 1.00 |
| 113_A | 124_V | 1.663 | 1.00 |
| 288_K | 291_M | 1.644 | 1.00 |
| 64_T | 118_Y | 1.637 | 1.00 |
| 299_V | 357_L | 1.626 | 1.00 |
| 57_K | 184_S | 1.615 | 1.00 |
| 268_Y | 398_G | 1.606 | 1.00 |
| 179_Q | 287_S | 1.605 | 1.00 |
| 91_A | 94_R | 1.599 | 1.00 |
| 120_C | 124_V | 1.582 | 1.00 |
| 284_F | 288_K | 1.565 | 1.00 |
| 104_S | 191_G | 1.563 | 1.00 |
| 38_D | 56_A | 1.556 | 1.00 |
| 308_G | 312_D | 1.527 | 1.00 |
| 36_I | 65_V | 1.509 | 1.00 |
| 60_W | 64_T | 1.492 | 1.00 |
| 86_I | 90_L | 1.485 | 1.00 |
| 299_V | 303_I | 1.467 | 1.00 |
| 94_R | 207_E | 1.464 | 1.00 |
| 248_F | 254_Y | 1.464 | 1.00 |
| 94_R | 98_A | 1.463 | 1.00 |
| 63_E | 410_K | 1.450 | 1.00 |
| 110_I | 124_V | 1.439 | 1.00 |
| 109_L | 112_S | 1.435 | 1.00 |
| 70_G | 399_M | 1.430 | 1.00 |
| 98_A | 102_L | 1.429 | 1.00 |
| 74_W | 399_M | 1.427 | 1.00 |
| 21_G | 96_F | 1.419 | 1.00 |
| 14_I | 146_W | 1.405 | 0.99 |
| 303_I | 361_V | 1.392 | 0.99 |
| 87_A | 92_A | 1.391 | 0.99 |
| 90_L | 95_V | 1.382 | 0.99 |
| 57_K | 183_W | 1.372 | 0.99 |
| 154_R | 309_Q | 1.371 | 0.99 |
| 113_A | 116_V | 1.357 | 0.99 |
| 143_W | 159_S | 1.348 | 0.99 |
| 105_T | 109_L | 1.344 | 0.99 |
| 277_Y | 282_F | 1.336 | 0.99 |
| 91_A | 95_V | 1.336 | 0.99 |
| 15_A | 147_A | 1.333 | 0.99 |
| 188_Y | 192_S | 1.331 | 0.99 |
| 119_G | 122_I | 1.323 | 0.99 |
| 26_F | 163_S | 1.322 | 0.99 |
| 75_G | 129_G | 1.320 | 0.99 |
| 62_P | 410_K | 1.312 | 0.99 |
| 88_S | 385_I | 1.310 | 0.99 |
| 109_L | 120_C | 1.291 | 0.99 |
| 35_A | 178_V | 1.290 | 0.99 |
| 154_R | 158_T | 1.280 | 0.99 |
| 306_I | 309_Q | 1.278 | 0.99 |
| 257_I | 389_I | 1.276 | 0.99 |
| 23_C | 166_G | 1.272 | 0.99 |
| 154_R | 312_D | 1.270 | 0.99 |
| 92_A | 207_E | 1.270 | 0.99 |
| 144_S | 152_R | 1.269 | 0.99 |
| 23_C | 169_I | 1.248 | 0.99 |
| 97_G | 101_L | 1.244 | 0.98 |
| 310_I | 314_L | 1.241 | 0.98 |
| 266_T | 428_H | 1.238 | 0.98 |
| 123_F | 127_L | 1.237 | 0.98 |
| 72_F | 132_E | 1.234 | 0.98 |
| 40_V | 65_V | 1.233 | 0.98 |
| 192_S | 196_V | 1.233 | 0.98 |
| 17_M | 197_W | 1.232 | 0.98 |
| 279_E | 286_I | 1.230 | 0.98 |
| 284_F | 292_L | 1.230 | 0.98 |
| 110_I | 187_F | 1.226 | 0.98 |
| 99_A | 131_V | 1.224 | 0.98 |
| 139_C | 159_S | 1.218 | 0.98 |
| 254_Y | 258_V | 1.217 | 0.98 |
| 102_L | 106_L | 1.217 | 0.98 |
| 79_T | 82_P | 1.212 | 0.98 |
| 29_R | 76_Y | 1.209 | 0.98 |
| 407_A | 411_N | 1.200 | 0.98 |
| 77_I | 399_M | 1.199 | 0.98 |
| 106_L | 128_Q | 1.196 | 0.98 |
| 12_Y | 16_I | 1.186 | 0.98 |
| 107_N | 190_Y | 1.181 | 0.98 |
| 88_S | 92_A | 1.174 | 0.98 |
| 164_Y | 300_M | 1.172 | 0.98 |
| 38_D | 57_K | 1.165 | 0.97 |
| 20_L | 197_W | 1.163 | 0.97 |
| 35_A | 186_V | 1.162 | 0.97 |
| 173_L | 176_I | 1.159 | 0.97 |
| 406_G | 410_K | 1.158 | 0.97 |
| 75_G | 79_T | 1.157 | 0.97 |
| 19_G | 158_T | 1.151 | 0.97 |
| 18_S | 139_C | 1.149 | 0.97 |
| 21_G | 135_T | 1.137 | 0.97 |
| 408_M | 412_K | 1.136 | 0.97 |
| 397_S | 401_C | 1.135 | 0.97 |
| 104_S | 195_M | 1.132 | 0.97 |
| 97_G | 201_W | 1.131 | 0.97 |
| 315_R | 319_I | 1.129 | 0.97 |
| 153_S | 308_G | 1.128 | 0.97 |
| 95_V | 98_A | 1.124 | 0.97 |
| 343_V | 355_S | 1.123 | 0.97 |
| 273_S | 406_G | 1.121 | 0.97 |
| 94_R | 97_G | 1.120 | 0.96 |
| 404_I | 407_A | 1.111 | 0.96 |
| 246_K | 249_T | 1.110 | 0.96 |
| 277_Y | 421_F | 1.102 | 0.96 |
| 221_R | 225_E | 1.098 | 0.96 |
| 426_L | 430_G | 1.095 | 0.96 |
| 108_M | 188_Y | 1.095 | 0.96 |
| 120_C | 123_F | 1.094 | 0.96 |
| 112_S | 188_Y | 1.093 | 0.96 |
| 277_Y | 281_V | 1.089 | 0.96 |
| 315_R | 318_Q | 1.089 | 0.96 |
| 220_R | 224_E | 1.088 | 0.96 |
| 216_T | 219_E | 1.086 | 0.96 |
| 67_M | 71_S | 1.081 | 0.95 |
| 80_Q | 391_N | 1.080 | 0.95 |
| 260_N | 390_S | 1.079 | 0.95 |
| 199_M | 202_L | 1.075 | 0.95 |
| 35_A | 39_M | 1.073 | 0.95 |
| 412_K | 416_E | 1.068 | 0.95 |
| 92_A | 141_G | 1.068 | 0.95 |
| 12_Y | 147_A | 1.068 | 0.95 |
| 264_S | 394_G | 1.068 | 0.95 |
| 278_F | 284_F | 1.066 | 0.95 |
| 145_K | 383_A | 1.066 | 0.95 |
| 178_V | 186_V | 1.061 | 0.95 |
| 200_F | 204_V | 1.060 | 0.95 |
| 298_L | 302_I | 1.055 | 0.95 |
| 149_P | 152_R | 1.049 | 0.94 |
| 146_W | 209_P | 1.047 | 0.94 |
| 68_I | 118_Y | 1.045 | 0.94 |
| 422_L | 425_A | 1.040 | 0.94 |
| 306_I | 310_I | 1.036 | 0.94 |
| 82_P | 85_Y | 1.034 | 0.94 |
| 157_T | 161_C | 1.030 | 0.94 |
| 90_L | 94_R | 1.029 | 0.94 |
| 303_I | 306_I | 1.027 | 0.94 |
| 260_N | 394_G | 1.025 | 0.93 |
| 251_M | 255_A | 1.024 | 0.93 |
| 27_G | 170_A | 1.020 | 0.93 |
| 123_F | 126_I | 1.019 | 0.93 |
| 177_L | 181_T | 1.017 | 0.93 |
| 185_S | 188_Y | 1.016 | 0.93 |
| 276_A | 280_E | 1.015 | 0.93 |
| 27_G | 190_Y | 1.011 | 0.93 |
| 278_F | 282_F | 1.010 | 0.93 |
| 278_F | 292_L | 1.009 | 0.93 |
| 269_L | 424_A | 1.009 | 0.93 |
| 15_A | 155_L | 1.007 | 0.93 |
| 177_L | 186_V | 1.004 | 0.93 |
| 35_A | 187_F | 1.002 | 0.92 |
| 338_A | 425_A | 1.002 | 0.92 |
| 262_C | 427_V | 1.001 | 0.92 |
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 | |
| 1pw4A | 1 | 0.8807 | 100 | 0.313 | Contact Map |
| 4j05A | 2 | 0.8091 | 100 | 0.359 | Contact Map |
| 3wdoA | 1 | 0.8807 | 100 | 0.364 | Contact Map |
| 3o7qA | 1 | 0.8308 | 100 | 0.371 | Contact Map |
| 2gfpA | 2 | 0.8048 | 100 | 0.382 | Contact Map |
| 4pypA | 1 | 0.872 | 100 | 0.395 | Contact Map |
| 2cfqA | 1 | 0.8764 | 100 | 0.411 | Contact Map |
| 4ldsA | 2 | 0.8829 | 100 | 0.414 | Contact Map |
| 4zw9A | 1 | 0 | 100 | 0.42 | Contact Map |
| 4gc0A | 1 | 0.9154 | 100 | 0.42 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)