| TM32 100-450 |
| ID: | 1488356924 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 351 (351) | ||
| Sequences: | 490 (319.4) | ||
| Seq/Len: | 1.396 | ||
| Nf(neff/√len): | 17.0 |
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: 1.396).
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 |
| 237_N | 240_I | 2.694 | 1.00 |
| 138_D | 246_T | 2.532 | 1.00 |
| 138_D | 142_F | 2.460 | 1.00 |
| 48_K | 51_E | 2.383 | 1.00 |
| 259_K | 262_R | 2.076 | 0.98 |
| 11_Y | 15_L | 2.055 | 0.98 |
| 180_Y | 184_Y | 2.032 | 0.98 |
| 184_Y | 187_V | 2.014 | 0.98 |
| 255_N | 259_K | 1.977 | 0.97 |
| 47_E | 50_R | 1.955 | 0.97 |
| 48_K | 67_W | 1.837 | 0.96 |
| 259_K | 265_L | 1.772 | 0.94 |
| 237_N | 241_A | 1.731 | 0.93 |
| 154_G | 161_L | 1.700 | 0.93 |
| 19_N | 108_I | 1.686 | 0.92 |
| 125_L | 135_M | 1.669 | 0.92 |
| 154_G | 179_P | 1.656 | 0.91 |
| 36_I | 40_Y | 1.629 | 0.90 |
| 154_G | 158_Q | 1.582 | 0.89 |
| 273_P | 280_I | 1.569 | 0.88 |
| 266_I | 280_I | 1.545 | 0.87 |
| 280_I | 284_H | 1.526 | 0.86 |
| 185_G | 188_F | 1.495 | 0.84 |
| 262_R | 266_I | 1.494 | 0.84 |
| 73_N | 76_D | 1.486 | 0.84 |
| 115_L | 119_F | 1.481 | 0.84 |
| 186_E | 189_A | 1.473 | 0.83 |
| 281_I | 285_M | 1.464 | 0.83 |
| 320_K | 328_Q | 1.447 | 0.82 |
| 44_L | 51_E | 1.416 | 0.80 |
| 72_W | 76_D | 1.409 | 0.79 |
| 15_L | 18_F | 1.400 | 0.79 |
| 1_I | 5_W | 1.396 | 0.78 |
| 227_Y | 259_K | 1.395 | 0.78 |
| 229_L | 234_L | 1.391 | 0.78 |
| 185_G | 192_I | 1.379 | 0.77 |
| 152_S | 279_L | 1.375 | 0.77 |
| 239_L | 243_F | 1.369 | 0.76 |
| 6_F | 39_S | 1.365 | 0.76 |
| 325_F | 329_C | 1.358 | 0.76 |
| 40_Y | 47_E | 1.356 | 0.76 |
| 48_K | 73_N | 1.356 | 0.76 |
| 48_K | 76_D | 1.347 | 0.75 |
| 129_V | 132_I | 1.346 | 0.75 |
| 101_R | 127_P | 1.336 | 0.74 |
| 43_T | 281_I | 1.329 | 0.73 |
| 76_D | 83_F | 1.329 | 0.73 |
| 233_I | 237_N | 1.326 | 0.73 |
| 262_R | 277_P | 1.325 | 0.73 |
| 331_E | 336_E | 1.318 | 0.73 |
| 119_F | 144_I | 1.318 | 0.73 |
| 233_I | 240_I | 1.318 | 0.73 |
| 330_I | 334_F | 1.312 | 0.72 |
| 76_D | 114_R | 1.310 | 0.72 |
| 246_T | 272_R | 1.309 | 0.72 |
| 116_L | 130_M | 1.309 | 0.72 |
| 235_L | 239_L | 1.307 | 0.72 |
| 273_P | 284_H | 1.293 | 0.71 |
| 332_E | 335_R | 1.293 | 0.71 |
| 246_T | 261_Q | 1.284 | 0.70 |
| 333_Y | 346_D | 1.277 | 0.69 |
| 331_E | 347_E | 1.277 | 0.69 |
| 235_L | 265_L | 1.275 | 0.69 |
| 232_N | 235_L | 1.275 | 0.69 |
| 185_G | 189_A | 1.268 | 0.68 |
| 132_I | 136_M | 1.255 | 0.67 |
| 94_Q | 236_V | 1.248 | 0.67 |
| 344_S | 348_R | 1.246 | 0.66 |
| 333_Y | 340_R | 1.245 | 0.66 |
| 51_E | 76_D | 1.239 | 0.66 |
| 247_F | 260_F | 1.239 | 0.66 |
| 17_L | 42_F | 1.232 | 0.65 |
| 340_R | 345_N | 1.224 | 0.64 |
| 324_D | 329_C | 1.211 | 0.63 |
| 184_Y | 188_F | 1.209 | 0.63 |
| 316_D | 339_D | 1.206 | 0.63 |
| 324_D | 327_E | 1.199 | 0.62 |
| 246_T | 266_I | 1.197 | 0.62 |
| 280_I | 283_S | 1.193 | 0.61 |
| 115_L | 144_I | 1.180 | 0.60 |
| 233_I | 236_V | 1.176 | 0.60 |
| 189_A | 192_I | 1.175 | 0.60 |
| 49_M | 281_I | 1.173 | 0.60 |
| 148_V | 177_Y | 1.170 | 0.59 |
| 246_T | 250_V | 1.170 | 0.59 |
| 347_E | 350_R | 1.168 | 0.59 |
| 109_I | 276_P | 1.160 | 0.58 |
| 113_I | 132_I | 1.154 | 0.58 |
| 235_L | 241_A | 1.153 | 0.58 |
| 322_V | 326_E | 1.152 | 0.57 |
| 327_E | 335_R | 1.151 | 0.57 |
| 340_R | 346_D | 1.150 | 0.57 |
| 179_P | 186_E | 1.149 | 0.57 |
| 182_M | 189_A | 1.143 | 0.57 |
| 51_E | 73_N | 1.143 | 0.57 |
| 180_Y | 229_L | 1.143 | 0.57 |
| 323_H | 327_E | 1.141 | 0.56 |
| 232_N | 246_T | 1.133 | 0.56 |
| 70_E | 79_A | 1.119 | 0.54 |
| 245_N | 254_S | 1.118 | 0.54 |
| 332_E | 343_S | 1.118 | 0.54 |
| 19_N | 112_Y | 1.115 | 0.54 |
| 331_E | 348_R | 1.113 | 0.54 |
| 155_V | 161_L | 1.113 | 0.54 |
| 35_W | 288_I | 1.111 | 0.53 |
| 227_Y | 241_A | 1.111 | 0.53 |
| 108_I | 112_Y | 1.110 | 0.53 |
| 184_Y | 189_A | 1.109 | 0.53 |
| 70_E | 73_N | 1.108 | 0.53 |
| 127_P | 135_M | 1.107 | 0.53 |
| 338_D | 346_D | 1.105 | 0.53 |
| 24_V | 47_E | 1.104 | 0.53 |
| 338_D | 345_N | 1.099 | 0.52 |
| 313_F | 318_E | 1.097 | 0.52 |
| 328_Q | 335_R | 1.087 | 0.51 |
| 268_T | 273_P | 1.086 | 0.51 |
| 321_K | 341_F | 1.080 | 0.50 |
| 223_I | 239_L | 1.077 | 0.50 |
| 230_V | 238_L | 1.074 | 0.50 |
| 229_L | 232_N | 1.074 | 0.50 |
| 255_N | 265_L | 1.074 | 0.50 |
| 343_S | 350_R | 1.074 | 0.50 |
| 183_I | 186_E | 1.072 | 0.49 |
| 84_S | 285_M | 1.071 | 0.49 |
| 86_G | 125_L | 1.071 | 0.49 |
| 102_V | 160_I | 1.070 | 0.49 |
| 319_L | 337_K | 1.069 | 0.49 |
| 263_Y | 280_I | 1.065 | 0.49 |
| 242_V | 246_T | 1.061 | 0.48 |
| 116_L | 134_K | 1.061 | 0.48 |
| 310_L | 313_F | 1.055 | 0.48 |
| 52_I | 67_W | 1.055 | 0.48 |
| 108_I | 132_I | 1.053 | 0.47 |
| 300_E | 304_D | 1.053 | 0.47 |
| 179_P | 182_M | 1.050 | 0.47 |
| 138_D | 242_V | 1.049 | 0.47 |
| 119_F | 122_N | 1.046 | 0.47 |
| 16_M | 222_A | 1.041 | 0.46 |
| 52_I | 118_I | 1.041 | 0.46 |
| 80_I | 106_V | 1.040 | 0.46 |
| 234_L | 241_A | 1.037 | 0.46 |
| 277_P | 280_I | 1.036 | 0.46 |
| 108_I | 155_V | 1.035 | 0.46 |
| 43_T | 280_I | 1.031 | 0.45 |
| 84_S | 88_I | 1.030 | 0.45 |
| 250_V | 274_V | 1.030 | 0.45 |
| 342_N | 345_N | 1.028 | 0.45 |
| 243_F | 263_Y | 1.026 | 0.45 |
| 330_I | 349_I | 1.024 | 0.45 |
| 310_L | 314_I | 1.023 | 0.44 |
| 332_E | 340_R | 1.021 | 0.44 |
| 224_M | 232_N | 1.021 | 0.44 |
| 235_L | 242_V | 1.020 | 0.44 |
| 312_L | 327_E | 1.019 | 0.44 |
| 344_S | 347_E | 1.019 | 0.44 |
| 231_A | 234_L | 1.019 | 0.44 |
| 114_R | 272_R | 1.018 | 0.44 |
| 327_E | 330_I | 1.016 | 0.44 |
| 182_M | 187_V | 1.013 | 0.43 |
| 90_R | 185_G | 1.013 | 0.43 |
| 79_A | 86_G | 1.012 | 0.43 |
| 298_K | 304_D | 1.011 | 0.43 |
| 196_C | 213_C | 1.008 | 0.43 |
| 4_F | 34_E | 1.004 | 0.43 |
| 40_Y | 230_V | 1.003 | 0.42 |
| 36_I | 282_F | 1.000 | 0.42 |
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 | |
| 3j9pD | 4 | 0.7778 | 100 | 0.588 | Contact Map |
| 3j5pB | 4 | 0.7009 | 100 | 0.637 | Contact Map |
| 4dxwA | 4 | 0.5983 | 99.7 | 0.815 | Contact Map |
| 3rvyA | 2 | 0.5926 | 99.6 | 0.833 | Contact Map |
| 4bgnA | 2 | 0.6011 | 99.5 | 0.846 | Contact Map |
| 2r9rB | 2 | 0.6353 | 98.5 | 0.897 | Contact Map |
| 3behA | 4 | 0.6296 | 98.3 | 0.904 | Contact Map |
| 4cbcA | 4 | 0.2621 | 97.2 | 0.924 | Contact Map |
| 4ltoA | 4 | 0.3903 | 97.1 | 0.925 | Contact Map |
| 1orqC | 1 | 0.5983 | 94.9 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)