| VgrG 500-841 |
| ID: | 1481894415 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 342 (331) | ||
| Sequences: | 1250 (783.3) | ||
| Seq/Len: | 3.776 | ||
| Nf(neff/√len): | 43.1 |
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: 3.776).
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 |
| 5_L | 18_L | 4.087 | 1.00 |
| 45_A | 53_I | 3.657 | 1.00 |
| 235_A | 248_C | 3.217 | 1.00 |
| 236_Y | 245_E | 2.939 | 1.00 |
| 68_Q | 80_E | 2.858 | 1.00 |
| 236_Y | 247_G | 2.739 | 1.00 |
| 207_S | 211_L | 2.692 | 1.00 |
| 10_K | 13_E | 2.590 | 1.00 |
| 4_K | 17_K | 2.585 | 1.00 |
| 23_G | 51_D | 2.538 | 1.00 |
| 156_S | 160_T | 2.489 | 1.00 |
| 57_G | 61_I | 2.436 | 1.00 |
| 312_D | 316_K | 2.409 | 1.00 |
| 227_E | 240_S | 2.249 | 1.00 |
| 140_A | 148_G | 2.154 | 1.00 |
| 147_S | 152_V | 2.150 | 1.00 |
| 210_N | 218_G | 2.021 | 1.00 |
| 238_K | 245_E | 2.005 | 1.00 |
| 227_E | 238_K | 1.948 | 1.00 |
| 65_A | 132_P | 1.948 | 1.00 |
| 219_K | 227_E | 1.933 | 1.00 |
| 53_I | 57_G | 1.901 | 1.00 |
| 28_L | 47_L | 1.889 | 1.00 |
| 240_S | 243_N | 1.874 | 1.00 |
| 311_T | 317_T | 1.847 | 1.00 |
| 317_T | 322_T | 1.809 | 0.99 |
| 243_N | 248_C | 1.785 | 0.99 |
| 7_M | 16_I | 1.752 | 0.99 |
| 61_I | 127_M | 1.711 | 0.99 |
| 312_D | 315_G | 1.659 | 0.99 |
| 33_N | 75_M | 1.654 | 0.99 |
| 256_S | 259_M | 1.651 | 0.99 |
| 184_G | 201_D | 1.624 | 0.99 |
| 1_A | 21_E | 1.621 | 0.99 |
| 53_I | 61_I | 1.610 | 0.98 |
| 81_A | 128_L | 1.576 | 0.98 |
| 172_A | 180_S | 1.565 | 0.98 |
| 235_A | 242_G | 1.526 | 0.98 |
| 317_T | 320_V | 1.503 | 0.97 |
| 35_D | 39_E | 1.503 | 0.97 |
| 229_I | 238_K | 1.503 | 0.97 |
| 176_V | 180_S | 1.494 | 0.97 |
| 58_G | 67_M | 1.493 | 0.97 |
| 235_A | 249_P | 1.481 | 0.97 |
| 6_R | 15_H | 1.465 | 0.97 |
| 8_E | 13_E | 1.453 | 0.97 |
| 297_Y | 309_G | 1.446 | 0.96 |
| 15_H | 32_H | 1.403 | 0.95 |
| 2_N | 21_E | 1.394 | 0.95 |
| 140_A | 143_L | 1.390 | 0.95 |
| 65_A | 131_A | 1.389 | 0.95 |
| 299_L | 317_T | 1.383 | 0.95 |
| 301_T | 317_T | 1.367 | 0.95 |
| 325_P | 328_V | 1.365 | 0.95 |
| 41_R | 46_E | 1.364 | 0.95 |
| 22_Y | 43_E | 1.360 | 0.94 |
| 238_K | 247_G | 1.338 | 0.94 |
| 190_A | 200_S | 1.336 | 0.94 |
| 1_A | 14_E | 1.329 | 0.93 |
| 77_D | 80_E | 1.326 | 0.93 |
| 21_E | 25_K | 1.320 | 0.93 |
| 193_R | 201_D | 1.314 | 0.93 |
| 193_R | 202_D | 1.311 | 0.93 |
| 2_N | 17_K | 1.305 | 0.93 |
| 78_M | 122_L | 1.299 | 0.92 |
| 13_E | 40_L | 1.292 | 0.92 |
| 201_D | 209_Q | 1.290 | 0.92 |
| 15_H | 36_A | 1.282 | 0.92 |
| 3_N | 16_I | 1.278 | 0.92 |
| 66_D | 130_H | 1.272 | 0.91 |
| 17_K | 21_E | 1.245 | 0.90 |
| 317_T | 325_P | 1.245 | 0.90 |
| 27_Q | 48_R | 1.240 | 0.90 |
| 235_A | 243_N | 1.240 | 0.90 |
| 36_A | 40_L | 1.239 | 0.90 |
| 254_L | 259_M | 1.238 | 0.90 |
| 3_N | 20_T | 1.238 | 0.90 |
| 322_T | 325_P | 1.237 | 0.90 |
| 317_T | 328_V | 1.228 | 0.89 |
| 309_G | 315_G | 1.215 | 0.89 |
| 319_P | 322_T | 1.212 | 0.89 |
| 292_Q | 295_T | 1.205 | 0.88 |
| 219_K | 229_I | 1.205 | 0.88 |
| 235_A | 241_G | 1.197 | 0.88 |
| 320_V | 325_P | 1.196 | 0.88 |
| 235_A | 246_L | 1.180 | 0.87 |
| 279_G | 282_F | 1.172 | 0.86 |
| 17_K | 25_K | 1.169 | 0.86 |
| 199_Q | 226_Q | 1.169 | 0.86 |
| 228_L | 232_C | 1.162 | 0.86 |
| 295_T | 317_T | 1.162 | 0.86 |
| 301_T | 320_V | 1.153 | 0.85 |
| 86_E | 89_L | 1.152 | 0.85 |
| 301_T | 319_P | 1.145 | 0.84 |
| 278_F | 282_F | 1.144 | 0.84 |
| 299_L | 320_V | 1.140 | 0.84 |
| 301_T | 305_D | 1.123 | 0.83 |
| 139_S | 148_G | 1.123 | 0.83 |
| 19_S | 27_Q | 1.119 | 0.82 |
| 64_S | 81_A | 1.116 | 0.82 |
| 17_K | 27_Q | 1.112 | 0.82 |
| 26_T | 51_D | 1.111 | 0.82 |
| 62_F | 66_D | 1.110 | 0.82 |
| 242_G | 245_E | 1.108 | 0.82 |
| 63_I | 129_L | 1.104 | 0.81 |
| 45_A | 61_I | 1.102 | 0.81 |
| 320_V | 323_S | 1.102 | 0.81 |
| 164_A | 168_F | 1.101 | 0.81 |
| 196_I | 205_M | 1.100 | 0.81 |
| 22_Y | 51_D | 1.099 | 0.81 |
| 29_N | 46_E | 1.095 | 0.81 |
| 122_L | 128_L | 1.094 | 0.80 |
| 185_M | 194_V | 1.079 | 0.79 |
| 221_T | 229_I | 1.076 | 0.79 |
| 4_K | 21_E | 1.076 | 0.79 |
| 235_A | 240_S | 1.076 | 0.79 |
| 272_V | 320_V | 1.073 | 0.79 |
| 86_E | 93_R | 1.070 | 0.78 |
| 195_N | 204_S | 1.070 | 0.78 |
| 26_T | 30_L | 1.060 | 0.77 |
| 188_L | 197_Q | 1.060 | 0.77 |
| 295_T | 298_R | 1.056 | 0.77 |
| 240_S | 248_C | 1.056 | 0.77 |
| 15_H | 21_E | 1.052 | 0.77 |
| 317_T | 323_S | 1.051 | 0.77 |
| 248_C | 256_S | 1.043 | 0.76 |
| 220_V | 228_L | 1.042 | 0.76 |
| 319_P | 325_P | 1.042 | 0.76 |
| 32_H | 38_R | 1.041 | 0.76 |
| 304_G | 317_T | 1.041 | 0.76 |
| 14_E | 17_K | 1.038 | 0.75 |
| 27_Q | 50_D | 1.036 | 0.75 |
| 301_T | 306_I | 1.035 | 0.75 |
| 153_G | 161_D | 1.034 | 0.75 |
| 23_G | 26_T | 1.028 | 0.74 |
| 213_I | 222_V | 1.026 | 0.74 |
| 202_D | 215_S | 1.026 | 0.74 |
| 248_C | 252_I | 1.025 | 0.74 |
| 320_V | 328_V | 1.021 | 0.74 |
| 91_L | 94_S | 1.020 | 0.74 |
| 4_K | 15_H | 1.019 | 0.73 |
| 270_A | 275_P | 1.011 | 0.73 |
| 183_Q | 187_L | 1.010 | 0.73 |
| 246_L | 252_I | 1.006 | 0.72 |
| 48_R | 71_A | 1.005 | 0.72 |
| 29_N | 48_R | 1.005 | 0.72 |
| 188_L | 195_N | 1.004 | 0.72 |
| 237_I | 244_I | 1.003 | 0.72 |
| 186_Q | 195_N | 1.001 | 0.72 |
| 294_S | 297_Y | 1.000 | 0.71 |
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 | |
| 4mtkA | 6 | 0.4649 | 98.4 | 0.903 | Contact Map |
| 1wthA | 1 | 0.5263 | 96.4 | 0.933 | Contact Map |
| 3a1mA | 6 | 0.3246 | 89.7 | 0.949 | Contact Map |
| 4ku0A | 3 | 0.269 | 59.3 | 0.962 | Contact Map |
| 2h0eA | 2 | 0.1959 | 43.9 | 0.965 | Contact Map |
| 2g2nA | 4 | 0.1959 | 33.3 | 0.967 | Contact Map |
| 1oo2A | 4 | 0.1959 | 23.5 | 0.97 | Contact Map |
| 3witA | 1 | 0.1842 | 23.3 | 0.97 | Contact Map |
| 1f86A | 2 | 0.193 | 20.6 | 0.97 | Contact Map |
| 3e8vA | 1 | 0.1842 | 18.8 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)