| VIPR-VIP |
| ID: | 1492350472 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 376 (375) | ||
| Sequences: | 691 (385.7) | ||
| Seq/Len: | 1.843 | ||
| Nf(neff/√len): | 19.9 |
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: 1.843).
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 |
| 352_C | 357_E | 2.623 | 1.00 |
| 352_C | 355_N | 2.600 | 1.00 |
| 31_D | 35_C | 2.483 | 1.00 |
| 39_T | 45_V | 2.203 | 0.99 |
| 351_Y | 357_E | 2.186 | 0.99 |
| 277_C | 280_R | 2.132 | 0.99 |
| 351_Y | 355_N | 1.993 | 0.99 |
| 355_N | 358_V | 1.968 | 0.99 |
| 353_F | 357_E | 1.914 | 0.98 |
| 31_D | 36_W | 1.871 | 0.98 |
| 124_T | 142_M | 1.767 | 0.97 |
| 112_G | 120_L | 1.741 | 0.96 |
| 34_T | 47_L | 1.736 | 0.96 |
| 71_E | 79_G | 1.696 | 0.95 |
| 31_D | 50_P | 1.686 | 0.95 |
| 344_G | 347_V | 1.678 | 0.95 |
| 72_G | 81_Y | 1.643 | 0.94 |
| 361_E | 366_W | 1.619 | 0.94 |
| 112_G | 116_S | 1.607 | 0.93 |
| 344_G | 352_C | 1.586 | 0.93 |
| 344_G | 355_N | 1.567 | 0.92 |
| 347_V | 357_E | 1.566 | 0.92 |
| 344_G | 357_E | 1.546 | 0.92 |
| 260_I | 264_I | 1.539 | 0.91 |
| 286_L | 297_S | 1.532 | 0.91 |
| 72_G | 85_C | 1.519 | 0.91 |
| 352_C | 358_V | 1.504 | 0.90 |
| 354_L | 357_E | 1.489 | 0.89 |
| 179_K | 245_D | 1.487 | 0.89 |
| 361_E | 364_R | 1.483 | 0.89 |
| 240_R | 246_T | 1.477 | 0.89 |
| 307_L | 311_P | 1.470 | 0.89 |
| 28_N | 38_A | 1.460 | 0.88 |
| 229_P | 236_W | 1.457 | 0.88 |
| 187_Y | 199_E | 1.452 | 0.88 |
| 137_R | 141_H | 1.438 | 0.87 |
| 195_W | 199_E | 1.435 | 0.87 |
| 309_L | 314_G | 1.429 | 0.87 |
| 153_T | 157_I | 1.415 | 0.86 |
| 275_F | 302_L | 1.410 | 0.86 |
| 347_V | 355_N | 1.405 | 0.85 |
| 147_S | 192_N | 1.396 | 0.85 |
| 116_S | 120_L | 1.394 | 0.85 |
| 30_W | 35_C | 1.386 | 0.84 |
| 35_C | 50_P | 1.386 | 0.84 |
| 112_G | 123_A | 1.386 | 0.84 |
| 13_L | 26_I | 1.371 | 0.83 |
| 305_S | 336_E | 1.368 | 0.83 |
| 31_D | 49_C | 1.358 | 0.83 |
| 112_G | 126_I | 1.357 | 0.83 |
| 85_C | 90_K | 1.354 | 0.82 |
| 113_H | 123_A | 1.352 | 0.82 |
| 359_Q | 366_W | 1.323 | 0.80 |
| 353_F | 358_V | 1.318 | 0.80 |
| 113_H | 120_L | 1.308 | 0.79 |
| 196_L | 207_L | 1.303 | 0.79 |
| 192_N | 195_W | 1.303 | 0.79 |
| 351_Y | 358_V | 1.293 | 0.78 |
| 348_A | 352_C | 1.285 | 0.78 |
| 4_A | 12_R | 1.269 | 0.76 |
| 302_L | 305_S | 1.251 | 0.75 |
| 178_C | 199_E | 1.248 | 0.75 |
| 16_Q | 19_V | 1.235 | 0.74 |
| 11_T | 26_I | 1.235 | 0.74 |
| 116_S | 130_F | 1.232 | 0.73 |
| 119_A | 161_I | 1.228 | 0.73 |
| 136_T | 147_S | 1.226 | 0.73 |
| 8_D | 12_R | 1.224 | 0.73 |
| 116_S | 123_A | 1.222 | 0.72 |
| 4_A | 9_N | 1.221 | 0.72 |
| 17_M | 25_S | 1.220 | 0.72 |
| 134_H | 138_N | 1.218 | 0.72 |
| 344_G | 348_A | 1.217 | 0.72 |
| 199_E | 226_W | 1.214 | 0.72 |
| 216_K | 318_I | 1.211 | 0.71 |
| 36_W | 50_P | 1.200 | 0.70 |
| 4_A | 8_D | 1.195 | 0.70 |
| 258_W | 262_A | 1.195 | 0.70 |
| 71_E | 81_Y | 1.192 | 0.70 |
| 153_T | 234_I | 1.186 | 0.69 |
| 20_K | 25_S | 1.181 | 0.69 |
| 249_W | 263_P | 1.180 | 0.69 |
| 13_L | 28_N | 1.179 | 0.69 |
| 116_S | 126_I | 1.177 | 0.68 |
| 127_L | 232_F | 1.176 | 0.68 |
| 36_W | 49_C | 1.172 | 0.68 |
| 17_M | 24_N | 1.170 | 0.68 |
| 9_N | 14_R | 1.169 | 0.68 |
| 271_N | 285_K | 1.168 | 0.67 |
| 72_G | 79_G | 1.167 | 0.67 |
| 11_T | 28_N | 1.166 | 0.67 |
| 9_N | 19_V | 1.164 | 0.67 |
| 218_F | 221_Y | 1.163 | 0.67 |
| 351_Y | 354_L | 1.162 | 0.67 |
| 204_H | 209_V | 1.158 | 0.67 |
| 238_I | 242_Y | 1.156 | 0.66 |
| 19_V | 23_L | 1.155 | 0.66 |
| 21_K | 26_I | 1.154 | 0.66 |
| 185_F | 313_F | 1.152 | 0.66 |
| 35_C | 49_C | 1.145 | 0.65 |
| 4_A | 17_M | 1.144 | 0.65 |
| 200_G | 203_L | 1.142 | 0.65 |
| 199_E | 203_L | 1.137 | 0.64 |
| 136_T | 140_I | 1.135 | 0.64 |
| 181_A | 213_S | 1.129 | 0.64 |
| 199_E | 225_G | 1.129 | 0.64 |
| 9_N | 12_R | 1.127 | 0.63 |
| 148_F | 151_R | 1.126 | 0.63 |
| 278_I | 282_L | 1.125 | 0.63 |
| 282_L | 286_L | 1.125 | 0.63 |
| 303_A | 310_I | 1.124 | 0.63 |
| 141_H | 144_L | 1.117 | 0.62 |
| 138_N | 151_R | 1.117 | 0.62 |
| 4_A | 15_K | 1.117 | 0.62 |
| 348_A | 357_E | 1.112 | 0.62 |
| 119_A | 345_F | 1.105 | 0.61 |
| 239_I | 259_I | 1.104 | 0.61 |
| 9_N | 15_K | 1.098 | 0.60 |
| 12_R | 19_V | 1.097 | 0.60 |
| 364_R | 367_G | 1.095 | 0.60 |
| 257_W | 261_K | 1.092 | 0.60 |
| 18_A | 21_K | 1.090 | 0.60 |
| 352_C | 356_G | 1.089 | 0.59 |
| 73_W | 131_R | 1.084 | 0.59 |
| 178_C | 195_W | 1.082 | 0.59 |
| 68_C | 85_C | 1.079 | 0.58 |
| 12_R | 17_M | 1.078 | 0.58 |
| 187_Y | 195_W | 1.078 | 0.58 |
| 12_R | 15_K | 1.076 | 0.58 |
| 72_G | 80_P | 1.074 | 0.58 |
| 16_Q | 23_L | 1.073 | 0.58 |
| 65_S | 84_A | 1.073 | 0.58 |
| 3_D | 7_T | 1.070 | 0.57 |
| 197_L | 264_I | 1.070 | 0.57 |
| 133_L | 141_H | 1.068 | 0.57 |
| 142_M | 356_G | 1.067 | 0.57 |
| 196_L | 275_F | 1.065 | 0.57 |
| 186_Q | 191_A | 1.065 | 0.57 |
| 29_M | 38_A | 1.061 | 0.57 |
| 136_T | 139_Y | 1.061 | 0.57 |
| 345_F | 349_I | 1.061 | 0.57 |
| 12_R | 16_Q | 1.058 | 0.56 |
| 39_T | 43_Q | 1.055 | 0.56 |
| 358_V | 361_E | 1.046 | 0.55 |
| 20_K | 23_L | 1.044 | 0.55 |
| 291_V | 296_S | 1.042 | 0.54 |
| 8_D | 17_M | 1.042 | 0.54 |
| 359_Q | 364_R | 1.038 | 0.54 |
| 4_A | 14_R | 1.038 | 0.54 |
| 15_K | 25_S | 1.037 | 0.54 |
| 191_A | 221_Y | 1.037 | 0.54 |
| 4_A | 19_V | 1.037 | 0.54 |
| 309_L | 312_L | 1.037 | 0.54 |
| 344_G | 358_V | 1.035 | 0.54 |
| 272_F | 280_R | 1.034 | 0.54 |
| 195_W | 225_G | 1.034 | 0.54 |
| 8_D | 15_K | 1.033 | 0.53 |
| 24_N | 27_L | 1.033 | 0.53 |
| 148_F | 158_K | 1.031 | 0.53 |
| 6_F | 14_R | 1.029 | 0.53 |
| 20_K | 24_N | 1.028 | 0.53 |
| 15_K | 19_V | 1.026 | 0.53 |
| 112_G | 119_A | 1.022 | 0.52 |
| 9_N | 17_M | 1.022 | 0.52 |
| 120_L | 126_I | 1.021 | 0.52 |
| 30_W | 36_W | 1.021 | 0.52 |
| 192_N | 316_H | 1.021 | 0.52 |
| 21_K | 25_S | 1.021 | 0.52 |
| 202_Y | 225_G | 1.020 | 0.52 |
| 7_T | 10_Y | 1.018 | 0.52 |
| 19_V | 25_S | 1.016 | 0.52 |
| 2_S | 21_K | 1.015 | 0.52 |
| 49_C | 343_Q | 1.014 | 0.51 |
| 215_R | 218_F | 1.013 | 0.51 |
| 152_A | 158_K | 1.013 | 0.51 |
| 18_A | 24_N | 1.012 | 0.51 |
| 15_K | 20_K | 1.012 | 0.51 |
| 248_C | 263_P | 1.012 | 0.51 |
| 344_G | 351_Y | 1.011 | 0.51 |
| 198_V | 236_W | 1.005 | 0.50 |
| 123_A | 138_N | 1.004 | 0.50 |
| 133_L | 137_R | 1.003 | 0.50 |
| 35_C | 39_T | 1.001 | 0.50 |
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 | 0.6649 | 100 | 0.557 | Contact Map |
| 4l6rA | 1 | 0.9362 | 100 | 0.643 | Contact Map |
| 4jkvA | 2 | 0.867 | 99.9 | 0.805 | Contact Map |
| 4qinA | 1 | 0.7819 | 99.9 | 0.816 | Contact Map |
| 2jodA | 1 | 0.2473 | 99.7 | 0.859 | Contact Map |
| 3n94A | 1 | 0.2394 | 99.7 | 0.859 | Contact Map |
| 4hj0A | 2 | 0.2154 | 99.7 | 0.862 | Contact Map |
| 2qkhA | 1 | 0.2101 | 99.7 | 0.863 | Contact Map |
| 2x57A | 3 | 0.2287 | 99.7 | 0.864 | Contact Map |
| 2xdgA | 2 | 0.2181 | 99.7 | 0.864 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)