| VIPR1 Alignment |
| ID: | 1488052454 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 417 (377) | ||
| Sequences: | 704 (414.8) | ||
| Seq/Len: | 1.867 | ||
| Nf(neff/√len): | 21.4 |
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: 1.867).
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 |
| 349_C | 352_N | 3.337 | 1.00 |
| 349_C | 354_E | 2.870 | 1.00 |
| 29_D | 33_C | 2.594 | 1.00 |
| 274_C | 277_R | 2.557 | 1.00 |
| 348_Y | 354_E | 2.493 | 1.00 |
| 37_A | 43_V | 2.344 | 1.00 |
| 24_C | 33_C | 2.256 | 1.00 |
| 348_Y | 352_N | 2.245 | 1.00 |
| 350_F | 354_E | 2.190 | 0.99 |
| 24_C | 34_W | 2.173 | 0.99 |
| 24_C | 29_D | 2.078 | 0.99 |
| 71_S | 82_C | 2.070 | 0.99 |
| 352_N | 355_V | 2.070 | 0.99 |
| 183_Y | 195_E | 2.067 | 0.99 |
| 120_M | 138_M | 2.003 | 0.99 |
| 26_R | 36_E | 1.952 | 0.99 |
| 29_D | 34_W | 1.822 | 0.97 |
| 32_T | 45_R | 1.797 | 0.97 |
| 349_C | 355_V | 1.759 | 0.97 |
| 108_G | 116_L | 1.742 | 0.96 |
| 82_C | 87_N | 1.693 | 0.95 |
| 74_Y | 77_P | 1.637 | 0.94 |
| 272_F | 299_L | 1.635 | 0.94 |
| 302_S | 333_E | 1.611 | 0.94 |
| 351_L | 354_E | 1.608 | 0.94 |
| 341_G | 349_C | 1.600 | 0.93 |
| 143_S | 188_N | 1.557 | 0.92 |
| 257_I | 261_I | 1.555 | 0.92 |
| 349_C | 353_G | 1.500 | 0.90 |
| 112_S | 116_L | 1.499 | 0.90 |
| 299_L | 302_S | 1.481 | 0.89 |
| 358_E | 363_W | 1.480 | 0.89 |
| 109_H | 119_A | 1.477 | 0.89 |
| 341_G | 352_N | 1.465 | 0.89 |
| 115_A | 342_F | 1.456 | 0.88 |
| 195_E | 199_L | 1.456 | 0.88 |
| 108_G | 122_I | 1.455 | 0.88 |
| 133_R | 137_H | 1.452 | 0.88 |
| 71_S | 74_Y | 1.445 | 0.88 |
| 191_W | 195_E | 1.432 | 0.87 |
| 344_V | 352_N | 1.425 | 0.87 |
| 304_L | 308_P | 1.412 | 0.86 |
| 344_V | 354_E | 1.401 | 0.85 |
| 255_W | 259_T | 1.366 | 0.83 |
| 200_H | 274_C | 1.363 | 0.83 |
| 306_L | 311_G | 1.348 | 0.82 |
| 195_E | 222_W | 1.345 | 0.82 |
| 132_T | 143_S | 1.343 | 0.82 |
| 345_A | 349_C | 1.332 | 0.81 |
| 131_C | 144_F | 1.325 | 0.81 |
| 47_C | 340_Q | 1.322 | 0.81 |
| 29_D | 48_P | 1.318 | 0.80 |
| 350_F | 355_V | 1.313 | 0.80 |
| 283_L | 294_S | 1.312 | 0.80 |
| 68_Q | 230_T | 1.311 | 0.80 |
| 108_G | 112_S | 1.308 | 0.80 |
| 28_W | 31_I | 1.290 | 0.78 |
| 235_V | 256_I | 1.288 | 0.78 |
| 108_G | 115_A | 1.282 | 0.78 |
| 28_W | 33_C | 1.281 | 0.78 |
| 275_I | 279_L | 1.277 | 0.77 |
| 275_I | 283_L | 1.275 | 0.77 |
| 348_Y | 355_V | 1.275 | 0.77 |
| 200_H | 277_R | 1.272 | 0.77 |
| 24_C | 28_W | 1.271 | 0.77 |
| 377_K | 380_H | 1.270 | 0.77 |
| 345_A | 354_E | 1.265 | 0.76 |
| 134_N | 147_R | 1.261 | 0.76 |
| 192_L | 272_F | 1.260 | 0.76 |
| 196_G | 217_Y | 1.248 | 0.75 |
| 175_K | 241_D | 1.242 | 0.75 |
| 341_G | 344_V | 1.241 | 0.74 |
| 346_V | 351_L | 1.236 | 0.74 |
| 341_G | 354_E | 1.236 | 0.74 |
| 197_L | 271_L | 1.234 | 0.74 |
| 181_F | 310_F | 1.233 | 0.74 |
| 358_E | 361_R | 1.231 | 0.74 |
| 342_F | 346_V | 1.231 | 0.74 |
| 348_Y | 351_L | 1.228 | 0.73 |
| 137_H | 140_L | 1.223 | 0.73 |
| 361_R | 364_R | 1.221 | 0.73 |
| 62_T | 81_A | 1.209 | 0.72 |
| 149_I | 153_I | 1.208 | 0.72 |
| 134_N | 232_W | 1.204 | 0.71 |
| 236_R | 242_V | 1.203 | 0.71 |
| 188_N | 222_W | 1.202 | 0.71 |
| 132_T | 135_Y | 1.202 | 0.71 |
| 15_L | 26_R | 1.197 | 0.71 |
| 7_E | 10_Q | 1.197 | 0.71 |
| 183_Y | 199_L | 1.196 | 0.70 |
| 33_C | 48_P | 1.195 | 0.70 |
| 138_M | 353_G | 1.195 | 0.70 |
| 200_H | 205_I | 1.189 | 0.70 |
| 128_K | 134_N | 1.188 | 0.70 |
| 183_Y | 191_W | 1.178 | 0.69 |
| 129_L | 183_Y | 1.177 | 0.69 |
| 308_P | 340_Q | 1.176 | 0.69 |
| 212_K | 315_I | 1.172 | 0.68 |
| 129_L | 137_H | 1.170 | 0.68 |
| 192_L | 302_S | 1.170 | 0.68 |
| 9_S | 12_L | 1.169 | 0.68 |
| 195_E | 198_Y | 1.168 | 0.68 |
| 234_V | 237_I | 1.166 | 0.68 |
| 188_N | 313_H | 1.165 | 0.68 |
| 152_F | 302_S | 1.163 | 0.67 |
| 130_H | 134_N | 1.160 | 0.67 |
| 132_T | 136_I | 1.156 | 0.67 |
| 28_W | 52_R | 1.153 | 0.66 |
| 10_Q | 14_E | 1.150 | 0.66 |
| 122_I | 129_L | 1.150 | 0.66 |
| 141_F | 148_A | 1.148 | 0.66 |
| 133_R | 141_F | 1.147 | 0.66 |
| 70_W | 81_A | 1.147 | 0.66 |
| 190_F | 220_I | 1.145 | 0.66 |
| 144_F | 147_R | 1.142 | 0.65 |
| 112_S | 119_A | 1.141 | 0.65 |
| 118_A | 142_M | 1.133 | 0.64 |
| 347_L | 350_F | 1.129 | 0.64 |
| 306_L | 340_Q | 1.127 | 0.64 |
| 300_A | 307_I | 1.124 | 0.64 |
| 196_G | 199_L | 1.124 | 0.64 |
| 63_R | 69_G | 1.123 | 0.63 |
| 24_C | 48_P | 1.119 | 0.63 |
| 214_F | 217_Y | 1.118 | 0.63 |
| 283_L | 345_A | 1.118 | 0.63 |
| 316_M | 332_F | 1.118 | 0.63 |
| 24_C | 35_P | 1.116 | 0.63 |
| 188_N | 195_E | 1.115 | 0.63 |
| 51_F | 56_S | 1.115 | 0.63 |
| 217_Y | 274_C | 1.114 | 0.62 |
| 348_Y | 353_G | 1.114 | 0.62 |
| 136_I | 140_L | 1.110 | 0.62 |
| 153_I | 161_S | 1.108 | 0.62 |
| 175_K | 303_T | 1.105 | 0.62 |
| 123_L | 228_F | 1.103 | 0.61 |
| 174_C | 195_E | 1.101 | 0.61 |
| 254_W | 258_K | 1.099 | 0.61 |
| 269_F | 277_R | 1.097 | 0.61 |
| 245_W | 260_P | 1.096 | 0.61 |
| 112_S | 122_I | 1.093 | 0.60 |
| 70_W | 84_Y | 1.088 | 0.60 |
| 271_L | 275_I | 1.081 | 0.59 |
| 148_A | 154_K | 1.081 | 0.59 |
| 13_A | 16_V | 1.077 | 0.59 |
| 268_N | 282_K | 1.076 | 0.59 |
| 183_Y | 275_I | 1.069 | 0.58 |
| 188_N | 191_W | 1.068 | 0.58 |
| 194_V | 232_W | 1.066 | 0.57 |
| 188_N | 264_S | 1.065 | 0.57 |
| 268_N | 279_L | 1.059 | 0.57 |
| 345_A | 352_N | 1.054 | 0.56 |
| 81_A | 87_N | 1.054 | 0.56 |
| 11_C | 15_L | 1.051 | 0.56 |
| 234_V | 238_H | 1.051 | 0.56 |
| 191_W | 222_W | 1.044 | 0.55 |
| 376_M | 379_H | 1.044 | 0.55 |
| 192_L | 299_L | 1.044 | 0.55 |
| 65_C | 69_G | 1.043 | 0.55 |
| 225_P | 232_W | 1.041 | 0.55 |
| 193_L | 273_I | 1.039 | 0.55 |
| 131_C | 134_N | 1.037 | 0.54 |
| 197_L | 207_F | 1.036 | 0.54 |
| 329_K | 334_L | 1.033 | 0.54 |
| 13_A | 17_E | 1.032 | 0.54 |
| 178_M | 186_M | 1.032 | 0.54 |
| 70_W | 76_A | 1.032 | 0.54 |
| 71_S | 76_A | 1.030 | 0.54 |
| 33_C | 37_A | 1.026 | 0.53 |
| 149_I | 230_T | 1.026 | 0.53 |
| 144_F | 188_N | 1.024 | 0.53 |
| 193_L | 202_L | 1.023 | 0.53 |
| 192_L | 203_L | 1.023 | 0.53 |
| 310_F | 334_L | 1.022 | 0.53 |
| 134_N | 148_A | 1.022 | 0.53 |
| 272_F | 302_S | 1.019 | 0.52 |
| 128_K | 272_F | 1.019 | 0.52 |
| 83_G | 87_N | 1.018 | 0.52 |
| 10_Q | 16_V | 1.017 | 0.52 |
| 24_C | 47_C | 1.011 | 0.51 |
| 279_L | 283_L | 1.010 | 0.51 |
| 6_E | 10_Q | 1.008 | 0.51 |
| 65_C | 82_C | 1.008 | 0.51 |
| 134_N | 154_K | 1.007 | 0.51 |
| 281_Q | 305_L | 1.007 | 0.51 |
| 70_W | 87_N | 1.006 | 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 | 0.6019 | 100 | 0.556 | Contact Map |
| 4l6rA | 1 | 0.8585 | 100 | 0.639 | Contact Map |
| 4jkvA | 2 | 0.7962 | 100 | 0.8 | Contact Map |
| 4qinA | 1 | 0.7218 | 99.9 | 0.811 | Contact Map |
| 2qkhA | 1 | 0.2014 | 99.9 | 0.834 | Contact Map |
| 4hj0A | 2 | 0.199 | 99.9 | 0.835 | Contact Map |
| 3n94A | 1 | 0.2086 | 99.9 | 0.836 | Contact Map |
| 4rwfA | 1 | 0 | 99.9 | 0.841 | Contact Map |
| 3c5tA | 1 | 0.2086 | 99.9 | 0.843 | Contact Map |
| 2x57A | 3 | 0.2038 | 99.8 | 0.846 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)