| FXR1 |
| ID: | 1508455880 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 539 (272) | ||
| Sequences: | 3295 (1628.3) | ||
| Seq/Len: | 12.114 | ||
| Nf(neff/√len): | 98.7 |
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: 12.114).
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 |
| 306_E | 310_K | 3.309 | 1.00 |
| 234_I | 238_G | 2.717 | 1.00 |
| 243_Q | 247_V | 2.457 | 1.00 |
| 311_S | 350_L | 2.398 | 1.00 |
| 313_V | 343_S | 2.286 | 1.00 |
| 297_I | 301_G | 2.215 | 1.00 |
| 284_D | 348_Q | 2.172 | 1.00 |
| 266_G | 272_V | 2.143 | 1.00 |
| 249_G | 271_A | 2.068 | 1.00 |
| 303_V | 306_E | 2.029 | 1.00 |
| 149_D | 153_A | 2.011 | 1.00 |
| 235_G | 238_G | 1.945 | 1.00 |
| 298_G | 301_G | 1.895 | 1.00 |
| 250_V | 271_A | 1.884 | 1.00 |
| 348_Q | 352_E | 1.861 | 1.00 |
| 240_N | 243_Q | 1.859 | 1.00 |
| 339_G | 344_I | 1.858 | 1.00 |
| 241_I | 245_R | 1.758 | 1.00 |
| 248_P | 278_F | 1.721 | 1.00 |
| 173_A | 178_V | 1.720 | 1.00 |
| 345_G | 348_Q | 1.716 | 1.00 |
| 147_H | 151_K | 1.716 | 1.00 |
| 231_G | 238_G | 1.701 | 1.00 |
| 139_E | 142_A | 1.677 | 1.00 |
| 340_T | 343_S | 1.614 | 1.00 |
| 288_V | 335_F | 1.599 | 1.00 |
| 234_I | 241_I | 1.585 | 1.00 |
| 273_K | 276_R | 1.577 | 1.00 |
| 282_V | 344_I | 1.553 | 1.00 |
| 305_Q | 308_V | 1.519 | 1.00 |
| 174_S | 177_T | 1.514 | 1.00 |
| 339_G | 347_V | 1.474 | 1.00 |
| 230_M | 255_L | 1.467 | 1.00 |
| 154_V | 184_L | 1.464 | 1.00 |
| 297_I | 304_I | 1.440 | 1.00 |
| 307_I | 316_V | 1.436 | 1.00 |
| 276_R | 280_E | 1.435 | 1.00 |
| 310_K | 350_L | 1.432 | 1.00 |
| 161_Y | 169_M | 1.413 | 1.00 |
| 268_S | 271_A | 1.393 | 0.99 |
| 231_G | 235_G | 1.393 | 0.99 |
| 142_A | 147_H | 1.378 | 0.99 |
| 285_F | 334_P | 1.377 | 0.99 |
| 350_L | 353_Y | 1.370 | 0.99 |
| 289_P | 292_L | 1.370 | 0.99 |
| 133_V | 169_M | 1.361 | 0.99 |
| 312_G | 343_S | 1.353 | 0.99 |
| 293_V | 318_I | 1.328 | 0.99 |
| 247_V | 278_F | 1.323 | 0.99 |
| 230_M | 260_G | 1.321 | 0.99 |
| 226_R | 229_L | 1.320 | 0.99 |
| 242_Q | 246_K | 1.304 | 0.99 |
| 341_K | 345_G | 1.303 | 0.99 |
| 231_G | 234_I | 1.290 | 0.99 |
| 179_K | 182_N | 1.288 | 0.99 |
| 221_E | 276_R | 1.286 | 0.99 |
| 244_A | 253_I | 1.281 | 0.99 |
| 337_F | 348_Q | 1.280 | 0.99 |
| 225_V | 262_F | 1.280 | 0.99 |
| 248_P | 274_K | 1.278 | 0.99 |
| 181_V | 184_L | 1.276 | 0.99 |
| 150_F | 154_V | 1.274 | 0.99 |
| 232_L | 240_N | 1.266 | 0.99 |
| 255_L | 262_F | 1.257 | 0.99 |
| 178_V | 181_V | 1.252 | 0.99 |
| 275_A | 279_L | 1.244 | 0.98 |
| 287_Q | 334_P | 1.241 | 0.98 |
| 311_S | 346_N | 1.240 | 0.98 |
| 248_P | 275_A | 1.236 | 0.98 |
| 153_A | 184_L | 1.236 | 0.98 |
| 139_E | 143_N | 1.229 | 0.98 |
| 274_K | 277_G | 1.229 | 0.98 |
| 303_V | 354_H | 1.228 | 0.98 |
| 299_K | 302_K | 1.222 | 0.98 |
| 156_A | 171_L | 1.191 | 0.98 |
| 148_K | 152_K | 1.181 | 0.98 |
| 313_V | 337_F | 1.168 | 0.97 |
| 318_I | 335_F | 1.156 | 0.97 |
| 138_R | 162_H | 1.152 | 0.97 |
| 238_G | 241_I | 1.152 | 0.97 |
| 148_K | 151_K | 1.151 | 0.97 |
| 236_T | 239_S | 1.149 | 0.97 |
| 181_V | 185_S | 1.149 | 0.97 |
| 150_F | 159_I | 1.147 | 0.97 |
| 240_N | 245_R | 1.143 | 0.97 |
| 138_R | 161_Y | 1.142 | 0.97 |
| 250_V | 275_A | 1.136 | 0.97 |
| 224_V | 261_T | 1.135 | 0.97 |
| 219_F | 272_V | 1.131 | 0.97 |
| 293_V | 333_V | 1.129 | 0.97 |
| 177_T | 180_R | 1.127 | 0.97 |
| 269_A | 273_K | 1.123 | 0.97 |
| 313_V | 347_V | 1.122 | 0.97 |
| 284_D | 344_I | 1.112 | 0.96 |
| 250_V | 264_I | 1.112 | 0.96 |
| 337_F | 347_V | 1.102 | 0.96 |
| 141_C | 169_M | 1.101 | 0.96 |
| 337_F | 351_L | 1.101 | 0.96 |
| 350_L | 354_H | 1.098 | 0.96 |
| 253_I | 262_F | 1.093 | 0.96 |
| 132_D | 168_L | 1.090 | 0.96 |
| 370_Q | 373_E | 1.085 | 0.96 |
| 129_C | 182_N | 1.084 | 0.96 |
| 273_K | 277_G | 1.083 | 0.96 |
| 169_M | 173_A | 1.082 | 0.96 |
| 139_E | 144_E | 1.067 | 0.95 |
| 173_A | 181_V | 1.064 | 0.95 |
| 171_L | 184_L | 1.063 | 0.95 |
| 254_E | 263_R | 1.062 | 0.95 |
| 242_Q | 245_R | 1.062 | 0.95 |
| 244_A | 248_P | 1.060 | 0.95 |
| 307_I | 311_S | 1.059 | 0.95 |
| 156_A | 177_T | 1.059 | 0.95 |
| 304_I | 308_V | 1.052 | 0.95 |
| 187_M | 190_R | 1.052 | 0.95 |
| 270_D | 274_K | 1.047 | 0.94 |
| 369_L | 376_R | 1.045 | 0.94 |
| 231_G | 260_G | 1.041 | 0.94 |
| 295_K | 303_V | 1.040 | 0.94 |
| 171_L | 178_V | 1.036 | 0.94 |
| 369_L | 372_D | 1.034 | 0.94 |
| 367_E | 370_Q | 1.031 | 0.94 |
| 308_V | 354_H | 1.028 | 0.94 |
| 229_L | 233_A | 1.027 | 0.94 |
| 248_P | 253_I | 1.026 | 0.94 |
| 233_A | 244_A | 1.026 | 0.94 |
| 284_D | 345_G | 1.025 | 0.93 |
| 294_G | 333_V | 1.025 | 0.93 |
| 222_E | 261_T | 1.023 | 0.93 |
| 230_M | 293_V | 1.022 | 0.93 |
| 317_R | 320_G | 1.010 | 0.93 |
| 286_I | 355_I | 1.008 | 0.93 |
| 227_E | 260_G | 1.005 | 0.93 |
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 | |
| 4qw2A | 2 | 0.3729 | 100 | 0.688 | Contact Map |
| 3h8zA | 1 | 0.2041 | 100 | 0.808 | Contact Map |
| 2qndA | 2 | 0.2635 | 99.9 | 0.846 | Contact Map |
| 3krmA | 3 | 0.2542 | 99.9 | 0.853 | Contact Map |
| 2anrA | 1 | 0.2505 | 99.9 | 0.856 | Contact Map |
| 1j4wA | 1 | 0.2486 | 99.9 | 0.857 | Contact Map |
| 2jvzA | 1 | 0.2523 | 99.9 | 0.858 | Contact Map |
| 3n89A | 2 | 0.5158 | 99.9 | 0.861 | Contact Map |
| 2jzxA | 1 | 0.2542 | 99.9 | 0.861 | Contact Map |
| 1tuaA | 1 | 0.2839 | 99.8 | 0.874 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)