| VP2 |
| ID: | 1414275201 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 392 (380) | ||
| Sequences: | 464 (177.3) | ||
| Seq/Len: | 1.221 | ||
| Nf(neff/√len): | 9.1 |
HHblits Results: (2013_03)
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: 1.221).
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 |
| 126_A | 210_L | 3.228 | 1.00 |
| 126_A | 208_L | 2.652 | 1.00 |
| 198_I | 206_A | 2.491 | 1.00 |
| 125_F | 230_A | 2.257 | 0.99 |
| 121_A | 197_I | 2.213 | 0.99 |
| 192_V | 321_I | 2.166 | 0.98 |
| 37_R | 307_D | 2.084 | 0.98 |
| 323_T | 371_M | 2.067 | 0.98 |
| 197_I | 234_L | 1.816 | 0.94 |
| 73_K | 238_N | 1.806 | 0.94 |
| 210_L | 227_W | 1.793 | 0.93 |
| 318_L | 323_T | 1.758 | 0.92 |
| 208_L | 229_I | 1.712 | 0.91 |
| 126_A | 227_W | 1.693 | 0.90 |
| 313_K | 317_E | 1.691 | 0.90 |
| 367_L | 388_F | 1.676 | 0.90 |
| 82_L | 227_W | 1.651 | 0.89 |
| 123_G | 191_F | 1.646 | 0.89 |
| 150_P | 154_G | 1.640 | 0.89 |
| 110_V | 206_A | 1.628 | 0.88 |
| 34_A | 61_C | 1.625 | 0.88 |
| 114_A | 200_L | 1.617 | 0.88 |
| 115_S | 118_H | 1.593 | 0.87 |
| 100_Y | 119_Q | 1.580 | 0.86 |
| 129_E | 224_H | 1.577 | 0.86 |
| 61_C | 258_C | 1.566 | 0.85 |
| 321_I | 371_M | 1.543 | 0.84 |
| 318_L | 371_M | 1.525 | 0.83 |
| 63_F | 254_A | 1.519 | 0.83 |
| 312_V | 317_E | 1.517 | 0.83 |
| 224_H | 255_P | 1.466 | 0.80 |
| 208_L | 227_W | 1.458 | 0.79 |
| 118_H | 129_E | 1.456 | 0.79 |
| 127_V | 210_L | 1.445 | 0.78 |
| 4_I | 37_R | 1.411 | 0.76 |
| 3_N | 327_F | 1.404 | 0.75 |
| 148_A | 154_G | 1.396 | 0.75 |
| 125_F | 190_A | 1.379 | 0.74 |
| 145_Y | 150_P | 1.331 | 0.70 |
| 25_T | 94_Q | 1.316 | 0.69 |
| 48_N | 52_Q | 1.309 | 0.68 |
| 105_G | 118_H | 1.308 | 0.68 |
| 180_L | 183_N | 1.305 | 0.68 |
| 105_G | 129_E | 1.303 | 0.67 |
| 204_N | 258_C | 1.284 | 0.66 |
| 341_R | 379_Y | 1.276 | 0.65 |
| 26_Q | 195_H | 1.275 | 0.65 |
| 239_F | 243_S | 1.275 | 0.65 |
| 90_G | 93_G | 1.271 | 0.65 |
| 129_E | 255_P | 1.269 | 0.64 |
| 6_A | 154_G | 1.261 | 0.64 |
| 239_F | 242_E | 1.260 | 0.64 |
| 234_L | 241_S | 1.249 | 0.63 |
| 124_V | 249_I | 1.248 | 0.63 |
| 196_Q | 201_R | 1.246 | 0.62 |
| 361_P | 382_W | 1.236 | 0.61 |
| 17_T | 22_T | 1.231 | 0.61 |
| 353_P | 356_C | 1.228 | 0.61 |
| 213_V | 227_W | 1.223 | 0.60 |
| 217_S | 228_G | 1.221 | 0.60 |
| 193_F | 241_S | 1.221 | 0.60 |
| 235_A | 386_L | 1.220 | 0.60 |
| 232_L | 386_L | 1.216 | 0.60 |
| 145_Y | 154_G | 1.212 | 0.59 |
| 316_M | 355_L | 1.208 | 0.59 |
| 143_T | 147_N | 1.204 | 0.58 |
| 35_Y | 129_E | 1.203 | 0.58 |
| 99_H | 199_N | 1.189 | 0.57 |
| 103_R | 219_D | 1.189 | 0.57 |
| 99_H | 196_Q | 1.186 | 0.57 |
| 148_A | 185_T | 1.184 | 0.56 |
| 6_A | 150_P | 1.181 | 0.56 |
| 204_N | 207_T | 1.179 | 0.56 |
| 151_G | 154_G | 1.177 | 0.56 |
| 310_G | 314_N | 1.177 | 0.56 |
| 126_A | 213_V | 1.177 | 0.56 |
| 196_Q | 214_N | 1.175 | 0.56 |
| 284_Q | 321_I | 1.175 | 0.56 |
| 118_H | 255_P | 1.169 | 0.55 |
| 24_T | 33_V | 1.168 | 0.55 |
| 95_N | 119_Q | 1.166 | 0.55 |
| 105_G | 115_S | 1.166 | 0.55 |
| 3_N | 147_N | 1.164 | 0.55 |
| 193_F | 199_N | 1.161 | 0.54 |
| 100_Y | 239_F | 1.151 | 0.53 |
| 35_Y | 118_H | 1.149 | 0.53 |
| 82_L | 108_V | 1.149 | 0.53 |
| 115_S | 129_E | 1.148 | 0.53 |
| 12_R | 196_Q | 1.146 | 0.53 |
| 92_F | 204_N | 1.146 | 0.53 |
| 204_N | 217_S | 1.144 | 0.53 |
| 60_A | 340_Y | 1.143 | 0.52 |
| 22_T | 63_F | 1.132 | 0.51 |
| 247_I | 311_E | 1.131 | 0.51 |
| 71_W | 122_L | 1.131 | 0.51 |
| 110_V | 122_L | 1.128 | 0.51 |
| 239_F | 245_P | 1.127 | 0.51 |
| 86_L | 195_H | 1.127 | 0.51 |
| 362_A | 383_A | 1.127 | 0.51 |
| 196_Q | 203_N | 1.125 | 0.51 |
| 317_E | 386_L | 1.122 | 0.50 |
| 157_F | 182_G | 1.117 | 0.50 |
| 192_V | 371_M | 1.117 | 0.50 |
| 109_H | 116_K | 1.116 | 0.50 |
| 322_D | 326_P | 1.115 | 0.50 |
| 110_V | 124_V | 1.115 | 0.50 |
| 256_M | 264_R | 1.113 | 0.50 |
| 145_Y | 149_N | 1.111 | 0.49 |
| 129_E | 199_N | 1.111 | 0.49 |
| 112_C | 249_I | 1.111 | 0.49 |
| 6_A | 190_A | 1.110 | 0.49 |
| 115_S | 392_F | 1.109 | 0.49 |
| 4_I | 16_L | 1.106 | 0.49 |
| 10_S | 21_S | 1.092 | 0.48 |
| 289_D | 383_A | 1.092 | 0.48 |
| 319_A | 359_L | 1.087 | 0.47 |
| 73_K | 241_S | 1.085 | 0.47 |
| 2_P | 5_E | 1.084 | 0.47 |
| 255_P | 262_G | 1.083 | 0.47 |
| 109_H | 205_C | 1.081 | 0.46 |
| 210_L | 213_V | 1.080 | 0.46 |
| 143_T | 152_E | 1.078 | 0.46 |
| 191_F | 208_L | 1.077 | 0.46 |
| 290_N | 297_L | 1.077 | 0.46 |
| 13_V | 18_L | 1.075 | 0.46 |
| 92_F | 201_R | 1.073 | 0.46 |
| 51_D | 217_S | 1.072 | 0.46 |
| 272_Q | 312_V | 1.072 | 0.46 |
| 67_D | 351_D | 1.072 | 0.46 |
| 156_T | 335_N | 1.071 | 0.45 |
| 99_H | 262_G | 1.070 | 0.45 |
| 144_S | 147_N | 1.069 | 0.45 |
| 323_T | 377_N | 1.069 | 0.45 |
| 264_R | 280_P | 1.067 | 0.45 |
| 318_L | 375_I | 1.065 | 0.45 |
| 118_H | 224_H | 1.064 | 0.45 |
| 129_E | 196_Q | 1.064 | 0.45 |
| 155_G | 162_T | 1.064 | 0.45 |
| 119_Q | 238_N | 1.063 | 0.45 |
| 13_V | 361_P | 1.063 | 0.45 |
| 109_H | 198_I | 1.061 | 0.44 |
| 196_Q | 199_N | 1.061 | 0.44 |
| 288_A | 320_E | 1.059 | 0.44 |
| 160_T | 164_D | 1.059 | 0.44 |
| 292_Q | 318_L | 1.057 | 0.44 |
| 83_P | 200_L | 1.057 | 0.44 |
| 125_F | 191_F | 1.056 | 0.44 |
| 116_K | 124_V | 1.054 | 0.44 |
| 61_C | 260_F | 1.052 | 0.44 |
| 296_A | 345_S | 1.052 | 0.44 |
| 150_P | 163_P | 1.049 | 0.43 |
| 298_P | 314_N | 1.046 | 0.43 |
| 192_V | 196_Q | 1.044 | 0.43 |
| 57_D | 61_C | 1.043 | 0.43 |
| 353_P | 360_S | 1.043 | 0.43 |
| 202_T | 224_H | 1.042 | 0.43 |
| 115_S | 243_S | 1.041 | 0.43 |
| 95_N | 204_N | 1.039 | 0.42 |
| 6_A | 46_E | 1.039 | 0.42 |
| 103_R | 259_E | 1.039 | 0.42 |
| 19_G | 35_Y | 1.037 | 0.42 |
| 324_M | 379_Y | 1.033 | 0.42 |
| 118_H | 201_R | 1.031 | 0.42 |
| 105_G | 201_R | 1.029 | 0.41 |
| 233_P | 236_P | 1.029 | 0.41 |
| 337_M | 341_R | 1.027 | 0.41 |
| 119_Q | 204_N | 1.027 | 0.41 |
| 192_V | 234_L | 1.025 | 0.41 |
| 99_H | 217_S | 1.025 | 0.41 |
| 320_E | 347_K | 1.023 | 0.41 |
| 96_M | 106_Y | 1.020 | 0.41 |
| 93_G | 114_A | 1.019 | 0.40 |
| 149_N | 181_F | 1.019 | 0.40 |
| 192_V | 197_I | 1.018 | 0.40 |
| 1_S | 4_I | 1.016 | 0.40 |
| 372_L | 386_L | 1.015 | 0.40 |
| 248_P | 285_Y | 1.015 | 0.40 |
| 3_N | 144_S | 1.015 | 0.40 |
| 287_T | 297_L | 1.013 | 0.40 |
| 235_A | 240_A | 1.013 | 0.40 |
| 29_A | 280_P | 1.013 | 0.40 |
| 119_Q | 256_M | 1.011 | 0.40 |
| 182_G | 185_T | 1.011 | 0.40 |
| 142_H | 155_G | 1.009 | 0.40 |
| 150_P | 181_F | 1.009 | 0.40 |
| 142_H | 149_N | 1.008 | 0.39 |
| 112_C | 231_I | 1.006 | 0.39 |
| 101_L | 252_T | 1.003 | 0.39 |
| 140_T | 144_S | 1.002 | 0.39 |
| 108_V | 112_C | 1.002 | 0.39 |
| 105_G | 110_V | 1.001 | 0.39 |
| 309_P | 312_V | 1.000 | 0.39 |
| 35_Y | 224_H | 1.000 | 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 | |
| 1hxs2 | 1 | 0.6811 | 100 | 0.278 | Contact Map |
| 1pov0 | 1 | 0.6505 | 100 | 0.3 | Contact Map |
| 4gb32 | 1 | 0.648 | 100 | 0.301 | Contact Map |
| 1aym2 | 1 | 0.6429 | 100 | 0.305 | Contact Map |
| 1ncqB | 1 | 0.6505 | 100 | 0.306 | Contact Map |
| 3cjiC | 1 | 0.6378 | 100 | 0.337 | Contact Map |
| 1bev2 | 1 | 0.6224 | 100 | 0.338 | Contact Map |
| 4gmp0 | 1 | 0.5969 | 100 | 0.346 | Contact Map |
| 3vbhB | 1 | 0.6173 | 100 | 0.354 | Contact Map |
| 1tme2 | 1 | 0.6097 | 100 | 0.37 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)