| cgt251 1-440 |
| ID: | 1510558726 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 440 (417) | ||
| Sequences: | 14938 (7815.2) | ||
| Seq/Len: | 35.823 | ||
| Nf(neff/√len): | 382.7 |
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: 35.823).
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 |
| 64_G | 128_K | 5.127 | 1.00 |
| 126_H | 224_D | 4.487 | 1.00 |
| 124_A | 127_A | 4.396 | 1.00 |
| 119_Q | 221_L | 4.225 | 1.00 |
| 114_T | 117_D | 4.130 | 1.00 |
| 55_Q | 120_N | 4.051 | 1.00 |
| 26_S | 60_K | 3.894 | 1.00 |
| 124_A | 128_K | 3.741 | 1.00 |
| 55_Q | 117_D | 3.613 | 1.00 |
| 67_T | 128_K | 3.334 | 1.00 |
| 208_D | 241_S | 3.079 | 1.00 |
| 66_L | 71_V | 3.063 | 1.00 |
| 125_A | 132_V | 2.969 | 1.00 |
| 68_G | 392_Q | 2.963 | 1.00 |
| 351_T | 421_Y | 2.936 | 1.00 |
| 58_I | 124_A | 2.924 | 1.00 |
| 81_E | 107_K | 2.917 | 1.00 |
| 346_L | 391_I | 2.888 | 1.00 |
| 325_D | 362_T | 2.871 | 1.00 |
| 58_I | 120_N | 2.820 | 1.00 |
| 55_Q | 58_I | 2.749 | 1.00 |
| 125_A | 130_I | 2.637 | 1.00 |
| 74_I | 125_A | 2.636 | 1.00 |
| 164_L | 188_N | 2.604 | 1.00 |
| 61_I | 128_K | 2.560 | 1.00 |
| 118_F | 122_I | 2.531 | 1.00 |
| 420_I | 433_A | 2.514 | 1.00 |
| 350_L | 395_A | 2.432 | 1.00 |
| 122_I | 132_V | 2.410 | 1.00 |
| 365_Y | 387_A | 2.396 | 1.00 |
| 396_P | 400_C | 2.299 | 1.00 |
| 343_E | 390_V | 2.293 | 1.00 |
| 115_I | 221_L | 2.270 | 1.00 |
| 347_A | 390_V | 2.261 | 1.00 |
| 389_Q | 392_Q | 2.256 | 1.00 |
| 57_I | 121_L | 2.251 | 1.00 |
| 120_N | 124_A | 2.208 | 1.00 |
| 219_L | 252_V | 2.188 | 1.00 |
| 20_I | 57_I | 2.182 | 1.00 |
| 116_A | 119_Q | 2.124 | 1.00 |
| 209_V | 213_D | 2.097 | 1.00 |
| 16_V | 395_A | 2.087 | 1.00 |
| 410_Q | 422_E | 2.055 | 1.00 |
| 26_S | 59_N | 2.039 | 1.00 |
| 141_T | 162_T | 1.994 | 1.00 |
| 61_I | 125_A | 1.985 | 1.00 |
| 216_K | 245_A | 1.983 | 1.00 |
| 118_F | 223_I | 1.970 | 1.00 |
| 27_D | 33_N | 1.957 | 1.00 |
| 410_Q | 424_K | 1.930 | 1.00 |
| 141_T | 200_L | 1.929 | 1.00 |
| 422_E | 429_V | 1.927 | 1.00 |
| 123_A | 127_A | 1.919 | 1.00 |
| 118_F | 134_I | 1.918 | 1.00 |
| 57_I | 76_I | 1.904 | 1.00 |
| 72_T | 399_K | 1.898 | 1.00 |
| 351_T | 432_V | 1.894 | 1.00 |
| 81_E | 103_R | 1.884 | 1.00 |
| 324_I | 345_A | 1.881 | 1.00 |
| 15_D | 72_T | 1.880 | 1.00 |
| 106_K | 213_D | 1.858 | 1.00 |
| 117_D | 120_N | 1.851 | 1.00 |
| 106_K | 214_A | 1.849 | 1.00 |
| 84_Y | 96_A | 1.832 | 1.00 |
| 68_G | 388_Y | 1.826 | 1.00 |
| 81_E | 110_P | 1.794 | 1.00 |
| 76_I | 79_P | 1.773 | 1.00 |
| 217_M | 221_L | 1.772 | 1.00 |
| 55_Q | 59_N | 1.742 | 1.00 |
| 344_Q | 434_V | 1.739 | 1.00 |
| 401_N | 428_N | 1.733 | 1.00 |
| 17_I | 73_A | 1.709 | 1.00 |
| 107_K | 115_I | 1.693 | 1.00 |
| 417_D | 437_N | 1.691 | 1.00 |
| 106_K | 217_M | 1.671 | 1.00 |
| 348_F | 434_V | 1.648 | 1.00 |
| 201_N | 204_N | 1.644 | 1.00 |
| 388_Y | 392_Q | 1.630 | 1.00 |
| 136_F | 215_I | 1.624 | 1.00 |
| 403_A | 430_A | 1.591 | 1.00 |
| 393_K | 396_P | 1.588 | 1.00 |
| 200_L | 207_V | 1.583 | 1.00 |
| 422_E | 431_V | 1.579 | 1.00 |
| 79_P | 118_F | 1.579 | 1.00 |
| 60_K | 65_Y | 1.566 | 1.00 |
| 421_Y | 432_V | 1.565 | 1.00 |
| 66_L | 130_I | 1.562 | 1.00 |
| 412_R | 431_V | 1.560 | 1.00 |
| 14_T | 405_A | 1.556 | 1.00 |
| 424_K | 429_V | 1.550 | 1.00 |
| 133_I | 225_G | 1.547 | 1.00 |
| 212_K | 245_A | 1.544 | 1.00 |
| 144_A | 196_D | 1.538 | 1.00 |
| 106_K | 210_Y | 1.532 | 1.00 |
| 347_A | 394_L | 1.530 | 1.00 |
| 67_T | 130_I | 1.526 | 1.00 |
| 210_Y | 213_D | 1.522 | 1.00 |
| 119_Q | 220_D | 1.516 | 1.00 |
| 116_A | 120_N | 1.504 | 1.00 |
| 343_E | 387_A | 1.495 | 1.00 |
| 121_L | 125_A | 1.489 | 1.00 |
| 115_I | 217_M | 1.488 | 1.00 |
| 205_S | 209_V | 1.486 | 1.00 |
| 104_D | 107_K | 1.484 | 1.00 |
| 79_P | 134_I | 1.482 | 1.00 |
| 19_Q | 77_S | 1.420 | 1.00 |
| 108_T | 118_F | 1.419 | 1.00 |
| 141_T | 175_F | 1.417 | 1.00 |
| 54_W | 108_T | 1.413 | 1.00 |
| 253_F | 279_S | 1.406 | 0.99 |
| 76_I | 121_L | 1.403 | 0.99 |
| 392_Q | 396_P | 1.402 | 0.99 |
| 99_G | 112_Y | 1.394 | 0.99 |
| 79_P | 108_T | 1.386 | 0.99 |
| 182_D | 195_Y | 1.377 | 0.99 |
| 20_I | 25_F | 1.376 | 0.99 |
| 210_Y | 214_A | 1.343 | 0.99 |
| 299_N | 302_G | 1.342 | 0.99 |
| 138_P | 211_L | 1.332 | 0.99 |
| 202_H | 211_L | 1.325 | 0.99 |
| 206_T | 209_V | 1.319 | 0.99 |
| 412_R | 422_E | 1.317 | 0.99 |
| 401_N | 430_A | 1.310 | 0.99 |
| 131_K | 224_D | 1.309 | 0.99 |
| 65_Y | 388_Y | 1.303 | 0.99 |
| 16_V | 71_V | 1.297 | 0.99 |
| 389_Q | 393_K | 1.295 | 0.99 |
| 17_I | 321_V | 1.294 | 0.99 |
| 408_S | 424_K | 1.289 | 0.99 |
| 343_E | 386_T | 1.287 | 0.99 |
| 85_S | 196_D | 1.280 | 0.99 |
| 245_A | 248_N | 1.263 | 0.99 |
| 80_V | 102_A | 1.255 | 0.99 |
| 215_I | 242_F | 1.245 | 0.98 |
| 138_P | 228_M | 1.241 | 0.98 |
| 14_T | 406_Y | 1.236 | 0.98 |
| 158_Y | 161_G | 1.236 | 0.98 |
| 358_I | 391_I | 1.224 | 0.98 |
| 115_I | 119_Q | 1.219 | 0.98 |
| 73_A | 131_K | 1.217 | 0.98 |
| 118_F | 121_L | 1.201 | 0.98 |
| 222_G | 249_Y | 1.200 | 0.98 |
| 138_P | 214_A | 1.187 | 0.98 |
| 66_L | 74_I | 1.187 | 0.98 |
| 216_K | 220_D | 1.183 | 0.98 |
| 136_F | 226_I | 1.182 | 0.98 |
| 230_A | 233_H | 1.173 | 0.98 |
| 143_P | 198_A | 1.166 | 0.97 |
| 282_D | 322_T | 1.164 | 0.97 |
| 209_V | 245_A | 1.152 | 0.97 |
| 241_S | 245_A | 1.150 | 0.97 |
| 55_Q | 114_T | 1.147 | 0.97 |
| 15_D | 73_A | 1.140 | 0.97 |
| 81_E | 104_D | 1.135 | 0.97 |
| 257_E | 328_D | 1.134 | 0.97 |
| 229_D | 328_D | 1.131 | 0.97 |
| 53_D | 56_G | 1.127 | 0.97 |
| 246_V | 252_V | 1.119 | 0.96 |
| 243_M | 254_T | 1.115 | 0.96 |
| 323_F | 326_N | 1.114 | 0.96 |
| 243_M | 247_N | 1.108 | 0.96 |
| 64_G | 68_G | 1.108 | 0.96 |
| 119_Q | 123_A | 1.108 | 0.96 |
| 212_K | 241_S | 1.106 | 0.96 |
| 65_Y | 68_G | 1.100 | 0.96 |
| 22_T | 57_I | 1.096 | 0.96 |
| 71_V | 358_I | 1.096 | 0.96 |
| 397_L | 401_N | 1.086 | 0.96 |
| 17_I | 133_I | 1.083 | 0.96 |
| 58_I | 117_D | 1.081 | 0.95 |
| 143_P | 196_D | 1.080 | 0.95 |
| 85_S | 194_L | 1.076 | 0.95 |
| 61_I | 64_G | 1.065 | 0.95 |
| 125_A | 128_K | 1.065 | 0.95 |
| 54_W | 118_F | 1.055 | 0.95 |
| 58_I | 121_L | 1.050 | 0.94 |
| 321_V | 357_A | 1.048 | 0.94 |
| 134_I | 223_I | 1.044 | 0.94 |
| 80_V | 134_I | 1.044 | 0.94 |
| 324_I | 349_T | 1.043 | 0.94 |
| 102_A | 105_F | 1.033 | 0.94 |
| 238_W | 242_F | 1.025 | 0.93 |
| 73_A | 133_I | 1.025 | 0.93 |
| 227_R | 328_D | 1.025 | 0.93 |
| 69_M | 388_Y | 1.024 | 0.93 |
| 71_V | 130_I | 1.023 | 0.93 |
| 351_T | 404_I | 1.007 | 0.93 |
| 229_D | 257_E | 1.007 | 0.93 |
| 257_E | 327_H | 1.006 | 0.93 |
| 161_G | 210_Y | 1.004 | 0.93 |
| 83_I | 103_R | 1.003 | 0.93 |
| 281_L | 357_A | 1.000 | 0.92 |
| 373_D | 376_A | 1.000 | 0.92 |
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 | |
| 4jcmA | 1 | 0.9591 | 100 | 0.119 | Contact Map |
| 4jclA | 1 | 0.9864 | 100 | 0.121 | Contact Map |
| 3bmvA | 1 | 0.9864 | 100 | 0.122 | Contact Map |
| 1d3cA | 1 | 0.9864 | 100 | 0.123 | Contact Map |
| 1qhoA | 1 | 0.9727 | 100 | 0.124 | Contact Map |
| 1cygA | 1 | 0.9841 | 100 | 0.13 | Contact Map |
| 2wc7A | 1 | 0.9091 | 100 | 0.175 | Contact Map |
| 4e2oA | 1 | 0.8773 | 100 | 0.179 | Contact Map |
| 1j0hA | 2 | 0.9273 | 100 | 0.184 | Contact Map |
| 1ea9C | 2 | 0.9295 | 100 | 0.187 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)