| A1KR23_MOUSE |
| ID: | 1408920924 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 445 (397) | ||
| Sequences: | 567 (435.2) | ||
| Seq/Len: | 1.428 | ||
| Nf(neff/√len): | 21.8 |
Jackhmmer Results: (2014_04_16)
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: 1.428).
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 |
| 312_E | 315_R | 3.694 | 1.00 |
| 311_A | 314_A | 3.231 | 1.00 |
| 300_Q | 304_N | 3.187 | 1.00 |
| 311_A | 315_R | 2.791 | 1.00 |
| 300_Q | 305_N | 2.568 | 1.00 |
| 300_Q | 309_V | 2.364 | 0.99 |
| 304_N | 309_V | 2.303 | 0.99 |
| 394_N | 397_L | 2.011 | 0.98 |
| 62_R | 122_F | 1.980 | 0.98 |
| 217_S | 224_E | 1.979 | 0.98 |
| 237_D | 246_Y | 1.971 | 0.98 |
| 235_K | 238_I | 1.850 | 0.96 |
| 301_V | 305_N | 1.849 | 0.96 |
| 301_V | 304_N | 1.813 | 0.95 |
| 390_P | 394_N | 1.763 | 0.94 |
| 224_E | 236_E | 1.752 | 0.94 |
| 300_Q | 306_P | 1.747 | 0.94 |
| 95_Q | 98_T | 1.731 | 0.94 |
| 302_M | 305_N | 1.713 | 0.93 |
| 232_D | 236_E | 1.625 | 0.91 |
| 224_E | 235_K | 1.592 | 0.89 |
| 225_K | 236_E | 1.579 | 0.89 |
| 252_I | 273_S | 1.572 | 0.89 |
| 138_L | 161_I | 1.545 | 0.87 |
| 272_V | 277_A | 1.532 | 0.87 |
| 197_C | 203_S | 1.502 | 0.85 |
| 242_N | 245_K | 1.484 | 0.84 |
| 231_F | 236_E | 1.473 | 0.84 |
| 229_P | 232_D | 1.473 | 0.84 |
| 232_D | 235_K | 1.471 | 0.84 |
| 305_N | 309_V | 1.469 | 0.84 |
| 231_F | 235_K | 1.457 | 0.83 |
| 261_E | 281_W | 1.446 | 0.82 |
| 301_V | 309_V | 1.444 | 0.82 |
| 224_E | 232_D | 1.443 | 0.82 |
| 233_I | 236_E | 1.442 | 0.82 |
| 236_E | 246_Y | 1.438 | 0.82 |
| 304_N | 308_R | 1.433 | 0.81 |
| 225_K | 235_K | 1.429 | 0.81 |
| 227_A | 236_E | 1.427 | 0.81 |
| 240_Y | 243_C | 1.399 | 0.79 |
| 247_Y | 276_K | 1.397 | 0.79 |
| 143_L | 213_F | 1.396 | 0.79 |
| 259_A | 285_C | 1.394 | 0.79 |
| 260_S | 266_A | 1.394 | 0.79 |
| 390_P | 393_V | 1.393 | 0.79 |
| 300_Q | 307_K | 1.387 | 0.78 |
| 260_S | 276_K | 1.367 | 0.77 |
| 418_A | 423_L | 1.366 | 0.77 |
| 398_G | 402_A | 1.348 | 0.76 |
| 302_M | 306_P | 1.337 | 0.75 |
| 243_C | 246_Y | 1.336 | 0.75 |
| 300_Q | 308_R | 1.336 | 0.75 |
| 253_F | 284_A | 1.330 | 0.74 |
| 224_E | 231_F | 1.326 | 0.74 |
| 226_I | 236_E | 1.325 | 0.74 |
| 227_A | 235_K | 1.321 | 0.73 |
| 224_E | 229_P | 1.320 | 0.73 |
| 247_Y | 277_A | 1.317 | 0.73 |
| 227_A | 233_I | 1.314 | 0.73 |
| 237_D | 245_K | 1.312 | 0.73 |
| 224_E | 227_A | 1.309 | 0.72 |
| 240_Y | 245_K | 1.299 | 0.72 |
| 226_I | 235_K | 1.294 | 0.71 |
| 399_K | 402_A | 1.286 | 0.71 |
| 302_M | 309_V | 1.286 | 0.71 |
| 144_F | 282_L | 1.285 | 0.70 |
| 310_E | 315_R | 1.282 | 0.70 |
| 99_M | 106_F | 1.281 | 0.70 |
| 226_I | 237_D | 1.274 | 0.70 |
| 67_Y | 73_P | 1.263 | 0.69 |
| 236_E | 245_K | 1.261 | 0.68 |
| 316_I | 320_E | 1.257 | 0.68 |
| 420_R | 423_L | 1.252 | 0.68 |
| 104_N | 107_L | 1.237 | 0.66 |
| 393_V | 397_L | 1.226 | 0.65 |
| 217_S | 235_K | 1.220 | 0.65 |
| 233_I | 237_D | 1.217 | 0.64 |
| 181_L | 281_W | 1.206 | 0.63 |
| 319_A | 322_A | 1.204 | 0.63 |
| 94_I | 426_R | 1.203 | 0.63 |
| 390_P | 397_L | 1.197 | 0.63 |
| 225_K | 231_F | 1.196 | 0.62 |
| 232_D | 237_D | 1.191 | 0.62 |
| 183_C | 197_C | 1.183 | 0.61 |
| 304_N | 307_K | 1.182 | 0.61 |
| 220_P | 223_L | 1.182 | 0.61 |
| 111_W | 139_W | 1.173 | 0.60 |
| 276_K | 279_D | 1.172 | 0.60 |
| 397_L | 402_A | 1.172 | 0.60 |
| 331_K | 334_T | 1.170 | 0.60 |
| 364_L | 367_N | 1.169 | 0.60 |
| 272_V | 276_K | 1.168 | 0.60 |
| 239_E | 245_K | 1.168 | 0.60 |
| 254_S | 260_S | 1.166 | 0.60 |
| 413_V | 423_L | 1.161 | 0.59 |
| 229_P | 233_I | 1.160 | 0.59 |
| 390_P | 396_G | 1.159 | 0.59 |
| 252_I | 272_V | 1.159 | 0.59 |
| 386_C | 390_P | 1.158 | 0.59 |
| 225_K | 233_I | 1.156 | 0.59 |
| 235_K | 246_Y | 1.155 | 0.58 |
| 109_Q | 144_F | 1.153 | 0.58 |
| 226_I | 229_P | 1.152 | 0.58 |
| 320_E | 324_G | 1.152 | 0.58 |
| 321_Q | 324_G | 1.151 | 0.58 |
| 67_Y | 116_L | 1.141 | 0.57 |
| 305_N | 310_E | 1.130 | 0.56 |
| 318_K | 322_A | 1.130 | 0.56 |
| 224_E | 228_L | 1.122 | 0.55 |
| 239_E | 246_Y | 1.118 | 0.55 |
| 258_L | 292_S | 1.117 | 0.55 |
| 80_V | 210_D | 1.116 | 0.55 |
| 414_I | 423_L | 1.115 | 0.54 |
| 225_K | 242_N | 1.113 | 0.54 |
| 254_S | 286_L | 1.110 | 0.54 |
| 417_A | 425_A | 1.110 | 0.54 |
| 301_V | 306_P | 1.108 | 0.54 |
| 160_N | 269_L | 1.105 | 0.53 |
| 217_S | 236_E | 1.105 | 0.53 |
| 217_S | 220_P | 1.103 | 0.53 |
| 231_F | 242_N | 1.103 | 0.53 |
| 380_E | 385_D | 1.100 | 0.53 |
| 217_S | 227_A | 1.095 | 0.52 |
| 355_K | 358_C | 1.095 | 0.52 |
| 235_K | 243_C | 1.095 | 0.52 |
| 318_K | 321_Q | 1.094 | 0.52 |
| 146_A | 202_E | 1.094 | 0.52 |
| 247_Y | 250_T | 1.094 | 0.52 |
| 163_L | 190_F | 1.094 | 0.52 |
| 400_P | 404_N | 1.086 | 0.51 |
| 235_K | 242_N | 1.084 | 0.51 |
| 103_V | 181_L | 1.081 | 0.51 |
| 226_I | 242_N | 1.080 | 0.51 |
| 414_I | 422_D | 1.078 | 0.51 |
| 282_L | 293_L | 1.077 | 0.51 |
| 414_I | 420_R | 1.074 | 0.50 |
| 225_K | 246_Y | 1.070 | 0.50 |
| 237_D | 240_Y | 1.068 | 0.50 |
| 227_A | 231_F | 1.066 | 0.49 |
| 64_L | 88_I | 1.066 | 0.49 |
| 397_L | 400_P | 1.064 | 0.49 |
| 96_E | 106_F | 1.063 | 0.49 |
| 416_T | 419_K | 1.061 | 0.49 |
| 236_E | 240_Y | 1.059 | 0.49 |
| 224_E | 233_I | 1.059 | 0.49 |
| 204_F | 207_T | 1.057 | 0.49 |
| 320_E | 323_D | 1.057 | 0.49 |
| 64_L | 137_C | 1.057 | 0.49 |
| 228_L | 239_E | 1.054 | 0.48 |
| 252_I | 259_A | 1.052 | 0.48 |
| 94_I | 185_L | 1.052 | 0.48 |
| 254_S | 258_L | 1.049 | 0.48 |
| 338_T | 367_N | 1.038 | 0.47 |
| 145_F | 272_V | 1.038 | 0.47 |
| 231_F | 239_E | 1.038 | 0.47 |
| 386_C | 394_N | 1.036 | 0.46 |
| 193_D | 197_C | 1.034 | 0.46 |
| 199_M | 203_S | 1.028 | 0.46 |
| 326_G | 331_K | 1.027 | 0.45 |
| 359_T | 373_G | 1.023 | 0.45 |
| 374_S | 380_E | 1.022 | 0.45 |
| 173_V | 182_S | 1.019 | 0.45 |
| 217_S | 225_K | 1.018 | 0.45 |
| 239_E | 242_N | 1.018 | 0.45 |
| 58_N | 128_L | 1.017 | 0.44 |
| 217_S | 221_V | 1.016 | 0.44 |
| 317_A | 321_Q | 1.015 | 0.44 |
| 63_L | 73_P | 1.012 | 0.44 |
| 253_F | 256_L | 1.012 | 0.44 |
| 256_L | 259_A | 1.011 | 0.44 |
| 326_G | 329_A | 1.010 | 0.44 |
| 217_S | 232_D | 1.008 | 0.44 |
| 358_C | 362_S | 1.008 | 0.44 |
| 230_Q | 235_K | 1.007 | 0.43 |
| 334_T | 337_G | 1.007 | 0.43 |
| 397_L | 412_P | 1.006 | 0.43 |
| 208_T | 246_Y | 1.006 | 0.43 |
| 316_I | 324_G | 1.004 | 0.43 |
| 138_L | 199_M | 1.003 | 0.43 |
| 351_E | 356_K | 1.002 | 0.43 |
| 221_V | 236_E | 1.002 | 0.43 |
| 406_K | 409_P | 1.002 | 0.43 |
| 349_V | 377_R | 1.001 | 0.43 |
| 191_P | 195_Q | 1.001 | 0.43 |
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 | |
| 4aq5E | 1 | 0.6921 | 100 | 0.385 | Contact Map |
| 4aq5B | 1 | 0.6899 | 100 | 0.385 | Contact Map |
| 3rhwA | 5 | 0.636 | 100 | 0.387 | Contact Map |
| 4aq5C | 1 | 0.6809 | 100 | 0.392 | Contact Map |
| 4aq5A | 2 | 0.6921 | 100 | 0.398 | Contact Map |
| 4cofA | 5 | 0.6494 | 100 | 0.402 | Contact Map |
| 2bg9E | 1 | 0.6921 | 100 | 0.402 | Contact Map |
| 2bg9B | 1 | 0.6921 | 100 | 0.405 | Contact Map |
| 2bg9C | 1 | 0.6921 | 100 | 0.406 | Contact Map |
| 2bg9A | 2 | 0.6921 | 100 | 0.409 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)