| shgl1 |
| ID: | 1495241267 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 352 (351) | ||
| Sequences: | 427 (252.9) | ||
| Seq/Len: | 1.217 | ||
| Nf(neff/√len): | 13.5 |
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: 1.217).
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 |
| 330_G | 339_F | 2.643 | 1.00 |
| 311_F | 317_I | 2.545 | 1.00 |
| 303_P | 310_G | 2.067 | 0.98 |
| 339_F | 344_V | 2.011 | 0.97 |
| 297_A | 301_F | 1.949 | 0.96 |
| 327_W | 330_G | 1.949 | 0.96 |
| 1_M | 5_G | 1.893 | 0.95 |
| 8_K | 12_K | 1.848 | 0.95 |
| 27_T | 169_D | 1.818 | 0.94 |
| 1_M | 8_K | 1.738 | 0.92 |
| 194_K | 198_E | 1.694 | 0.90 |
| 337_G | 340_P | 1.643 | 0.89 |
| 64_S | 68_L | 1.642 | 0.89 |
| 5_G | 13_A | 1.632 | 0.88 |
| 327_W | 340_P | 1.624 | 0.88 |
| 147_H | 151_L | 1.616 | 0.87 |
| 299_Y | 343_Y | 1.613 | 0.87 |
| 5_G | 8_K | 1.605 | 0.87 |
| 9_Q | 12_K | 1.599 | 0.87 |
| 309_L | 340_P | 1.580 | 0.86 |
| 297_A | 311_F | 1.566 | 0.85 |
| 97_M | 105_G | 1.550 | 0.84 |
| 161_L | 164_R | 1.546 | 0.84 |
| 5_G | 9_Q | 1.535 | 0.84 |
| 15_Q | 19_E | 1.521 | 0.83 |
| 1_M | 13_A | 1.493 | 0.81 |
| 299_Y | 327_W | 1.492 | 0.81 |
| 315_D | 342_N | 1.490 | 0.81 |
| 319_L | 326_N | 1.480 | 0.80 |
| 2_S | 8_K | 1.478 | 0.80 |
| 134_E | 224_E | 1.466 | 0.80 |
| 317_I | 330_G | 1.462 | 0.79 |
| 25_E | 28_K | 1.462 | 0.79 |
| 330_G | 340_P | 1.427 | 0.77 |
| 4_A | 13_A | 1.420 | 0.76 |
| 94_A | 118_G | 1.401 | 0.75 |
| 8_K | 160_K | 1.380 | 0.74 |
| 295_C | 344_V | 1.368 | 0.73 |
| 334_G | 340_P | 1.358 | 0.72 |
| 331_M | 336_S | 1.357 | 0.72 |
| 161_L | 165_R | 1.352 | 0.71 |
| 246_Q | 250_Q | 1.351 | 0.71 |
| 255_Y | 259_P | 1.349 | 0.71 |
| 252_R | 258_K | 1.347 | 0.71 |
| 211_Q | 215_L | 1.341 | 0.70 |
| 340_P | 343_Y | 1.338 | 0.70 |
| 12_K | 15_Q | 1.332 | 0.70 |
| 171_K | 189_K | 1.328 | 0.69 |
| 194_K | 200_S | 1.326 | 0.69 |
| 327_W | 337_G | 1.322 | 0.69 |
| 160_K | 164_R | 1.312 | 0.68 |
| 318_T | 331_M | 1.308 | 0.68 |
| 33_F | 158_L | 1.299 | 0.67 |
| 174_R | 206_E | 1.292 | 0.66 |
| 327_W | 339_F | 1.290 | 0.66 |
| 317_I | 344_V | 1.288 | 0.66 |
| 143_L | 152_R | 1.285 | 0.66 |
| 346_I | 350_L | 1.285 | 0.66 |
| 161_L | 200_S | 1.284 | 0.66 |
| 1_M | 9_Q | 1.284 | 0.66 |
| 283_P | 287_G | 1.264 | 0.64 |
| 149_K | 225_Y | 1.261 | 0.64 |
| 160_K | 168_F | 1.257 | 0.63 |
| 327_W | 343_Y | 1.257 | 0.63 |
| 94_A | 101_G | 1.255 | 0.63 |
| 15_Q | 166_L | 1.252 | 0.63 |
| 297_A | 317_I | 1.251 | 0.63 |
| 315_D | 332_L | 1.249 | 0.62 |
| 336_S | 348_V | 1.247 | 0.62 |
| 58_L | 215_L | 1.246 | 0.62 |
| 223_L | 230_V | 1.237 | 0.61 |
| 96_A | 100_F | 1.235 | 0.61 |
| 296_R | 345_E | 1.234 | 0.61 |
| 146_L | 153_E | 1.232 | 0.61 |
| 2_S | 13_A | 1.229 | 0.61 |
| 1_M | 4_A | 1.223 | 0.60 |
| 299_Y | 340_P | 1.221 | 0.60 |
| 309_L | 337_G | 1.219 | 0.60 |
| 1_M | 6_L | 1.216 | 0.59 |
| 68_L | 73_T | 1.214 | 0.59 |
| 247_A | 251_P | 1.213 | 0.59 |
| 9_Q | 13_A | 1.210 | 0.59 |
| 299_Y | 309_L | 1.209 | 0.59 |
| 4_A | 7_K | 1.208 | 0.59 |
| 166_L | 174_R | 1.203 | 0.58 |
| 71_I | 81_E | 1.198 | 0.58 |
| 1_M | 12_K | 1.198 | 0.58 |
| 94_A | 97_M | 1.197 | 0.58 |
| 193_S | 197_A | 1.197 | 0.58 |
| 156_H | 167_D | 1.194 | 0.57 |
| 2_S | 5_G | 1.192 | 0.57 |
| 68_L | 74_M | 1.192 | 0.57 |
| 158_L | 200_S | 1.191 | 0.57 |
| 224_E | 231_Q | 1.189 | 0.57 |
| 187_L | 204_L | 1.186 | 0.57 |
| 97_M | 101_G | 1.186 | 0.57 |
| 189_K | 193_S | 1.185 | 0.56 |
| 328_Y | 351_P | 1.184 | 0.56 |
| 72_N | 85_G | 1.178 | 0.56 |
| 142_P | 167_D | 1.171 | 0.55 |
| 195_E | 200_S | 1.168 | 0.55 |
| 33_F | 37_E | 1.166 | 0.55 |
| 32_D | 194_K | 1.162 | 0.54 |
| 190_F | 205_L | 1.161 | 0.54 |
| 23_G | 26_G | 1.158 | 0.54 |
| 298_L | 327_W | 1.153 | 0.53 |
| 68_L | 71_I | 1.145 | 0.53 |
| 33_F | 259_P | 1.142 | 0.52 |
| 211_Q | 214_Q | 1.138 | 0.52 |
| 314_G | 337_G | 1.137 | 0.52 |
| 13_A | 16_K | 1.135 | 0.52 |
| 309_L | 330_G | 1.134 | 0.52 |
| 20_K | 27_T | 1.125 | 0.51 |
| 70_M | 74_M | 1.124 | 0.51 |
| 168_F | 255_Y | 1.122 | 0.50 |
| 146_L | 151_L | 1.117 | 0.50 |
| 296_R | 316_I | 1.117 | 0.50 |
| 23_G | 37_E | 1.115 | 0.50 |
| 11_H | 14_T | 1.114 | 0.50 |
| 3_V | 10_F | 1.113 | 0.49 |
| 19_E | 165_R | 1.112 | 0.49 |
| 295_C | 339_F | 1.112 | 0.49 |
| 182_E | 319_L | 1.109 | 0.49 |
| 218_L | 248_S | 1.100 | 0.48 |
| 3_V | 6_L | 1.100 | 0.48 |
| 71_I | 74_M | 1.100 | 0.48 |
| 99_K | 103_E | 1.098 | 0.48 |
| 22_G | 222_Q | 1.096 | 0.48 |
| 30_D | 142_P | 1.094 | 0.48 |
| 151_L | 168_F | 1.092 | 0.47 |
| 22_G | 204_L | 1.090 | 0.47 |
| 70_M | 73_T | 1.089 | 0.47 |
| 187_L | 246_Q | 1.085 | 0.47 |
| 74_M | 85_G | 1.084 | 0.47 |
| 294_C | 351_P | 1.082 | 0.46 |
| 143_L | 151_L | 1.079 | 0.46 |
| 215_L | 240_L | 1.078 | 0.46 |
| 12_K | 167_D | 1.073 | 0.46 |
| 160_K | 182_E | 1.073 | 0.46 |
| 322_Q | 328_Y | 1.071 | 0.45 |
| 12_K | 183_L | 1.070 | 0.45 |
| 17_V | 21_V | 1.069 | 0.45 |
| 308_E | 340_P | 1.068 | 0.45 |
| 73_T | 85_G | 1.067 | 0.45 |
| 77_I | 80_Q | 1.064 | 0.45 |
| 40_V | 161_L | 1.064 | 0.45 |
| 164_R | 182_E | 1.059 | 0.44 |
| 160_K | 163_G | 1.055 | 0.44 |
| 222_Q | 229_A | 1.054 | 0.44 |
| 101_G | 159_K | 1.053 | 0.44 |
| 309_L | 314_G | 1.052 | 0.44 |
| 33_F | 80_Q | 1.051 | 0.43 |
| 309_L | 334_G | 1.050 | 0.43 |
| 59_Q | 140_I | 1.045 | 0.43 |
| 110_F | 233_L | 1.044 | 0.43 |
| 154_I | 204_L | 1.039 | 0.42 |
| 203_N | 210_E | 1.036 | 0.42 |
| 16_K | 154_I | 1.034 | 0.42 |
| 143_L | 166_L | 1.033 | 0.42 |
| 164_R | 189_K | 1.032 | 0.42 |
| 305_N | 308_E | 1.031 | 0.42 |
| 10_F | 221_A | 1.024 | 0.41 |
| 154_I | 158_L | 1.022 | 0.41 |
| 22_G | 30_D | 1.020 | 0.40 |
| 142_P | 146_L | 1.019 | 0.40 |
| 156_H | 305_N | 1.017 | 0.40 |
| 29_L | 190_F | 1.015 | 0.40 |
| 181_E | 214_Q | 1.013 | 0.40 |
| 161_L | 194_K | 1.012 | 0.40 |
| 309_L | 319_L | 1.011 | 0.40 |
| 48_M | 229_A | 1.010 | 0.40 |
| 21_V | 121_M | 1.008 | 0.39 |
| 49_E | 96_A | 1.006 | 0.39 |
| 114_L | 161_L | 1.006 | 0.39 |
| 281_G | 284_K | 1.004 | 0.39 |
| 231_Q | 238_V | 1.003 | 0.39 |
| 276_G | 279_H | 1.003 | 0.39 |
| 309_L | 327_W | 1.001 | 0.39 |
| 315_D | 330_G | 1.001 | 0.39 |
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 | |
| 1zwwA | 2 | 0.5739 | 100 | 0.506 | Contact Map |
| 2z0vA | 2 | 0.6392 | 100 | 0.576 | Contact Map |
| 4atmA | 1 | 0.5881 | 100 | 0.621 | Contact Map |
| 1uruA | 1 | 0.5682 | 100 | 0.624 | Contact Map |
| 2ficA | 2 | 0.5312 | 100 | 0.635 | Contact Map |
| 4avmA | 1 | 0.6108 | 100 | 0.641 | Contact Map |
| 4bneA | 2 | 0.5767 | 99.9 | 0.74 | Contact Map |
| 1opkA | 1 | 0.1705 | 99.8 | 0.761 | Contact Map |
| 1ug1A | 1 | 0.2159 | 99.8 | 0.762 | Contact Map |
| 2pz1A | 1 | 0.2102 | 99.8 | 0.765 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)