| VIPR MSA |
| ID: | 1490629289 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 349 (349) | ||
| Sequences: | 665 (368.7) | ||
| Seq/Len: | 1.905 | ||
| Nf(neff/√len): | 19.7 |
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: 1.905).
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 |
| 325_C | 328_N | 3.159 | 1.00 |
| 325_C | 330_E | 2.788 | 1.00 |
| 7_D | 11_C | 2.648 | 1.00 |
| 251_C | 254_R | 2.575 | 1.00 |
| 324_Y | 330_E | 2.457 | 1.00 |
| 2_C | 7_D | 2.338 | 1.00 |
| 15_A | 21_V | 2.299 | 1.00 |
| 328_N | 331_V | 2.263 | 1.00 |
| 2_C | 11_C | 2.198 | 1.00 |
| 324_Y | 328_N | 2.179 | 0.99 |
| 98_M | 116_M | 2.068 | 0.99 |
| 2_C | 12_W | 2.000 | 0.99 |
| 326_F | 330_E | 1.997 | 0.99 |
| 4_R | 14_E | 1.950 | 0.99 |
| 7_D | 12_W | 1.890 | 0.98 |
| 325_C | 331_V | 1.860 | 0.98 |
| 47_G | 60_C | 1.847 | 0.98 |
| 10_T | 23_R | 1.778 | 0.97 |
| 7_D | 26_P | 1.724 | 0.96 |
| 161_Y | 173_E | 1.720 | 0.96 |
| 86_G | 90_S | 1.714 | 0.96 |
| 86_G | 94_L | 1.648 | 0.95 |
| 327_L | 330_E | 1.643 | 0.95 |
| 60_C | 65_N | 1.595 | 0.93 |
| 232_W | 236_T | 1.589 | 0.93 |
| 249_F | 276_L | 1.573 | 0.93 |
| 173_E | 177_L | 1.549 | 0.92 |
| 48_W | 105_R | 1.487 | 0.90 |
| 110_T | 121_S | 1.487 | 0.90 |
| 324_Y | 327_L | 1.485 | 0.90 |
| 49_S | 105_R | 1.468 | 0.89 |
| 11_C | 26_P | 1.461 | 0.89 |
| 203_P | 210_W | 1.461 | 0.89 |
| 334_E | 339_W | 1.455 | 0.89 |
| 317_G | 325_C | 1.443 | 0.88 |
| 101_L | 206_F | 1.414 | 0.87 |
| 317_G | 320_V | 1.408 | 0.86 |
| 317_G | 328_N | 1.373 | 0.84 |
| 111_R | 115_H | 1.370 | 0.84 |
| 324_Y | 331_V | 1.347 | 0.83 |
| 57_A | 60_C | 1.330 | 0.82 |
| 281_L | 285_P | 1.329 | 0.82 |
| 195_Y | 251_C | 1.328 | 0.81 |
| 325_C | 329_G | 1.326 | 0.81 |
| 121_S | 166_N | 1.325 | 0.81 |
| 123_I | 321_A | 1.311 | 0.80 |
| 127_I | 131_I | 1.310 | 0.80 |
| 178_H | 251_C | 1.308 | 0.80 |
| 279_S | 309_E | 1.306 | 0.80 |
| 166_N | 290_H | 1.306 | 0.80 |
| 112_N | 125_R | 1.302 | 0.80 |
| 173_E | 200_W | 1.298 | 0.79 |
| 152_C | 173_E | 1.289 | 0.79 |
| 170_L | 249_F | 1.287 | 0.79 |
| 90_S | 94_L | 1.286 | 0.79 |
| 168_F | 198_I | 1.280 | 0.78 |
| 234_I | 238_I | 1.280 | 0.78 |
| 317_G | 330_E | 1.277 | 0.78 |
| 86_G | 100_I | 1.276 | 0.78 |
| 326_F | 331_V | 1.274 | 0.78 |
| 214_R | 220_V | 1.273 | 0.78 |
| 93_A | 318_F | 1.270 | 0.77 |
| 276_L | 279_S | 1.269 | 0.77 |
| 95_T | 123_I | 1.266 | 0.77 |
| 111_R | 119_F | 1.263 | 0.77 |
| 260_L | 271_S | 1.262 | 0.77 |
| 323_L | 326_F | 1.255 | 0.76 |
| 83_Y | 114_I | 1.248 | 0.76 |
| 334_E | 337_R | 1.247 | 0.75 |
| 2_C | 6_W | 1.244 | 0.75 |
| 169_W | 200_W | 1.244 | 0.75 |
| 192_F | 195_Y | 1.239 | 0.75 |
| 320_V | 330_E | 1.233 | 0.74 |
| 174_G | 177_L | 1.231 | 0.74 |
| 6_W | 9_I | 1.230 | 0.74 |
| 316_Q | 328_N | 1.227 | 0.74 |
| 112_N | 210_W | 1.224 | 0.74 |
| 152_C | 200_W | 1.221 | 0.73 |
| 283_L | 288_G | 1.215 | 0.73 |
| 212_V | 216_H | 1.213 | 0.73 |
| 153_K | 280_T | 1.211 | 0.72 |
| 49_S | 60_C | 1.210 | 0.72 |
| 96_A | 120_M | 1.208 | 0.72 |
| 175_L | 248_L | 1.201 | 0.72 |
| 169_W | 173_E | 1.200 | 0.71 |
| 321_A | 325_C | 1.195 | 0.71 |
| 12_W | 26_P | 1.192 | 0.71 |
| 131_I | 139_S | 1.188 | 0.70 |
| 127_I | 208_T | 1.187 | 0.70 |
| 106_K | 112_N | 1.184 | 0.70 |
| 213_V | 233_I | 1.174 | 0.69 |
| 84_T | 133_D | 1.168 | 0.68 |
| 46_Q | 208_T | 1.167 | 0.68 |
| 178_H | 254_R | 1.167 | 0.68 |
| 86_G | 93_A | 1.165 | 0.68 |
| 160_Q | 165_A | 1.158 | 0.68 |
| 59_A | 65_N | 1.157 | 0.67 |
| 223_W | 280_T | 1.149 | 0.67 |
| 90_S | 97_A | 1.148 | 0.67 |
| 101_L | 322_V | 1.147 | 0.66 |
| 119_F | 126_A | 1.140 | 0.66 |
| 190_K | 292_I | 1.140 | 0.66 |
| 116_M | 329_G | 1.139 | 0.66 |
| 61_G | 65_N | 1.138 | 0.66 |
| 152_C | 161_Y | 1.137 | 0.65 |
| 22_V | 38_N | 1.136 | 0.65 |
| 87_H | 97_A | 1.134 | 0.65 |
| 2_C | 26_P | 1.134 | 0.65 |
| 332_Q | 339_W | 1.133 | 0.65 |
| 161_Y | 200_W | 1.133 | 0.65 |
| 108_H | 112_N | 1.132 | 0.65 |
| 122_F | 125_R | 1.131 | 0.65 |
| 127_I | 336_K | 1.130 | 0.65 |
| 106_K | 249_F | 1.130 | 0.65 |
| 170_L | 276_L | 1.128 | 0.65 |
| 155_M | 187_S | 1.127 | 0.64 |
| 289_I | 297_F | 1.127 | 0.64 |
| 245_N | 259_K | 1.124 | 0.64 |
| 152_C | 169_W | 1.124 | 0.64 |
| 178_H | 183_I | 1.120 | 0.64 |
| 320_V | 328_N | 1.120 | 0.64 |
| 176_Y | 199_G | 1.119 | 0.64 |
| 311_V | 319_V | 1.116 | 0.63 |
| 109_C | 122_F | 1.112 | 0.63 |
| 173_E | 176_Y | 1.110 | 0.63 |
| 212_V | 215_I | 1.105 | 0.62 |
| 321_A | 330_E | 1.105 | 0.62 |
| 25_C | 316_Q | 1.103 | 0.62 |
| 175_L | 185_F | 1.101 | 0.62 |
| 130_F | 279_S | 1.100 | 0.62 |
| 153_K | 219_D | 1.096 | 0.61 |
| 6_W | 11_C | 1.094 | 0.61 |
| 305_K | 308_F | 1.093 | 0.61 |
| 269_E | 289_I | 1.093 | 0.61 |
| 256_L | 260_L | 1.089 | 0.61 |
| 249_F | 279_S | 1.088 | 0.60 |
| 161_Y | 169_W | 1.085 | 0.60 |
| 285_P | 328_N | 1.080 | 0.60 |
| 192_F | 198_I | 1.078 | 0.59 |
| 317_G | 331_V | 1.076 | 0.59 |
| 249_F | 334_E | 1.076 | 0.59 |
| 189_R | 192_F | 1.072 | 0.59 |
| 87_H | 94_L | 1.071 | 0.59 |
| 159_F | 287_F | 1.064 | 0.58 |
| 13_P | 26_P | 1.060 | 0.57 |
| 285_P | 316_Q | 1.060 | 0.57 |
| 277_A | 284_I | 1.058 | 0.57 |
| 252_I | 260_L | 1.056 | 0.57 |
| 212_V | 289_I | 1.055 | 0.57 |
| 181_L | 275_R | 1.055 | 0.57 |
| 337_R | 340_R | 1.053 | 0.57 |
| 7_D | 43_C | 1.052 | 0.57 |
| 171_L | 180_L | 1.051 | 0.56 |
| 112_N | 132_K | 1.049 | 0.56 |
| 209_A | 213_V | 1.046 | 0.56 |
| 95_T | 212_V | 1.046 | 0.56 |
| 166_N | 200_W | 1.046 | 0.56 |
| 124_M | 162_C | 1.046 | 0.56 |
| 56_Y | 60_C | 1.043 | 0.56 |
| 62_Y | 65_N | 1.041 | 0.55 |
| 233_I | 318_F | 1.040 | 0.55 |
| 170_L | 279_S | 1.039 | 0.55 |
| 107_L | 161_Y | 1.039 | 0.55 |
| 128_A | 275_R | 1.039 | 0.55 |
| 324_Y | 329_G | 1.037 | 0.55 |
| 253_I | 257_V | 1.032 | 0.54 |
| 231_W | 235_K | 1.030 | 0.54 |
| 161_Y | 177_L | 1.030 | 0.54 |
| 7_D | 25_C | 1.028 | 0.54 |
| 126_A | 132_K | 1.027 | 0.54 |
| 265_V | 270_T | 1.023 | 0.53 |
| 90_S | 104_F | 1.020 | 0.53 |
| 167_F | 272_Q | 1.019 | 0.53 |
| 90_S | 101_L | 1.019 | 0.53 |
| 286_L | 321_A | 1.018 | 0.53 |
| 112_N | 172_V | 1.017 | 0.53 |
| 293_M | 308_F | 1.017 | 0.53 |
| 121_S | 290_H | 1.013 | 0.52 |
| 2_C | 13_P | 1.011 | 0.52 |
| 317_G | 321_A | 1.010 | 0.52 |
| 22_V | 40_T | 1.008 | 0.52 |
| 166_N | 214_R | 1.001 | 0.51 |
| 281_L | 293_M | 1.000 | 0.51 |
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 | |
| 4k5yA | 3 | 0.7135 | 100 | 0.502 | Contact Map |
| 4l6rA | 1 | 0.9628 | 100 | 0.603 | Contact Map |
| 4jkvA | 2 | 0.8682 | 99.9 | 0.772 | Contact Map |
| 4qinA | 1 | 0.8138 | 99.9 | 0.788 | Contact Map |
| 2qkhA | 1 | 0.1777 | 99.8 | 0.828 | Contact Map |
| 4hj0A | 2 | 0.1748 | 99.8 | 0.83 | Contact Map |
| 4rwfA | 1 | 0 | 99.8 | 0.833 | Contact Map |
| 3c5tA | 1 | 0.1862 | 99.8 | 0.835 | Contact Map |
| 3n94A | 1 | 0.1862 | 99.8 | 0.835 | Contact Map |
| 4ersA | 1 | 0.1777 | 99.7 | 0.84 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)