| -CGT Bacillus circulans strain 251 1-407 |
| ID: | 1510567530 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 407 (395) | ||
| Sequences: | 12039 (5937.4) | ||
| Seq/Len: | 30.478 | ||
| Nf(neff/√len): | 298.7 |
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: 30.478).
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 | 5.070 | 1.00 |
| 124_A | 127_A | 4.528 | 1.00 |
| 126_H | 224_D | 4.429 | 1.00 |
| 114_T | 117_D | 4.206 | 1.00 |
| 119_Q | 221_L | 3.912 | 1.00 |
| 55_Q | 120_N | 3.719 | 1.00 |
| 26_S | 60_K | 3.668 | 1.00 |
| 67_T | 128_K | 3.650 | 1.00 |
| 124_A | 128_K | 3.625 | 1.00 |
| 55_Q | 117_D | 3.583 | 1.00 |
| 208_D | 241_S | 3.571 | 1.00 |
| 66_L | 71_V | 3.258 | 1.00 |
| 325_D | 362_T | 3.047 | 1.00 |
| 125_A | 132_V | 3.037 | 1.00 |
| 74_I | 125_A | 2.974 | 1.00 |
| 68_G | 392_Q | 2.884 | 1.00 |
| 346_L | 391_I | 2.837 | 1.00 |
| 58_I | 120_N | 2.827 | 1.00 |
| 81_E | 107_K | 2.825 | 1.00 |
| 58_I | 124_A | 2.730 | 1.00 |
| 125_A | 130_I | 2.659 | 1.00 |
| 55_Q | 58_I | 2.576 | 1.00 |
| 122_I | 132_V | 2.574 | 1.00 |
| 61_I | 128_K | 2.570 | 1.00 |
| 118_F | 122_I | 2.550 | 1.00 |
| 365_Y | 387_A | 2.505 | 1.00 |
| 350_L | 395_A | 2.505 | 1.00 |
| 219_L | 252_V | 2.499 | 1.00 |
| 120_N | 124_A | 2.332 | 1.00 |
| 20_I | 57_I | 2.279 | 1.00 |
| 115_I | 221_L | 2.265 | 1.00 |
| 343_E | 390_V | 2.261 | 1.00 |
| 27_D | 33_N | 2.258 | 1.00 |
| 216_K | 245_A | 2.237 | 1.00 |
| 57_I | 121_L | 2.189 | 1.00 |
| 16_V | 395_A | 2.169 | 1.00 |
| 324_I | 345_A | 2.127 | 1.00 |
| 396_P | 400_C | 2.108 | 1.00 |
| 15_D | 72_T | 2.088 | 1.00 |
| 117_D | 120_N | 2.078 | 1.00 |
| 76_I | 79_P | 2.063 | 1.00 |
| 116_A | 119_Q | 2.043 | 1.00 |
| 84_Y | 96_A | 2.015 | 1.00 |
| 61_I | 125_A | 2.003 | 1.00 |
| 118_F | 223_I | 1.921 | 1.00 |
| 118_F | 134_I | 1.914 | 1.00 |
| 17_I | 73_A | 1.901 | 1.00 |
| 81_E | 110_P | 1.889 | 1.00 |
| 57_I | 76_I | 1.880 | 1.00 |
| 209_V | 213_D | 1.827 | 1.00 |
| 106_K | 214_A | 1.816 | 1.00 |
| 26_S | 59_N | 1.815 | 1.00 |
| 123_A | 127_A | 1.810 | 1.00 |
| 141_T | 175_F | 1.802 | 1.00 |
| 217_M | 221_L | 1.788 | 1.00 |
| 55_Q | 59_N | 1.785 | 1.00 |
| 106_K | 217_M | 1.771 | 1.00 |
| 389_Q | 392_Q | 1.771 | 1.00 |
| 141_T | 200_L | 1.770 | 1.00 |
| 121_L | 125_A | 1.735 | 1.00 |
| 99_G | 112_Y | 1.707 | 1.00 |
| 79_P | 118_F | 1.705 | 1.00 |
| 201_N | 204_N | 1.693 | 1.00 |
| 81_E | 103_R | 1.689 | 1.00 |
| 106_K | 213_D | 1.667 | 1.00 |
| 107_K | 115_I | 1.653 | 1.00 |
| 136_F | 215_I | 1.649 | 1.00 |
| 200_L | 207_V | 1.632 | 1.00 |
| 215_I | 242_F | 1.619 | 1.00 |
| 20_I | 25_F | 1.612 | 1.00 |
| 119_Q | 220_D | 1.602 | 1.00 |
| 388_Y | 392_Q | 1.589 | 1.00 |
| 104_D | 107_K | 1.586 | 1.00 |
| 212_K | 245_A | 1.582 | 1.00 |
| 115_I | 217_M | 1.571 | 1.00 |
| 205_S | 209_V | 1.559 | 1.00 |
| 68_G | 388_Y | 1.539 | 1.00 |
| 60_K | 65_Y | 1.532 | 1.00 |
| 210_Y | 213_D | 1.527 | 1.00 |
| 116_A | 120_N | 1.526 | 1.00 |
| 66_L | 130_I | 1.524 | 1.00 |
| 347_A | 390_V | 1.522 | 1.00 |
| 80_V | 102_A | 1.520 | 1.00 |
| 108_T | 118_F | 1.494 | 1.00 |
| 79_P | 134_I | 1.493 | 1.00 |
| 54_W | 108_T | 1.492 | 1.00 |
| 72_T | 399_K | 1.490 | 1.00 |
| 202_H | 211_L | 1.487 | 1.00 |
| 14_T | 405_A | 1.472 | 1.00 |
| 222_G | 249_Y | 1.459 | 1.00 |
| 282_D | 322_T | 1.447 | 1.00 |
| 67_T | 130_I | 1.436 | 1.00 |
| 392_Q | 396_P | 1.433 | 1.00 |
| 212_K | 241_S | 1.429 | 1.00 |
| 323_F | 326_N | 1.428 | 1.00 |
| 206_T | 209_V | 1.416 | 1.00 |
| 19_Q | 77_S | 1.409 | 1.00 |
| 393_K | 396_P | 1.379 | 0.99 |
| 138_P | 214_A | 1.370 | 0.99 |
| 76_I | 121_L | 1.369 | 0.99 |
| 106_K | 210_Y | 1.367 | 0.99 |
| 17_I | 321_V | 1.362 | 0.99 |
| 133_I | 225_G | 1.356 | 0.99 |
| 66_L | 74_I | 1.354 | 0.99 |
| 358_I | 391_I | 1.351 | 0.99 |
| 16_V | 71_V | 1.344 | 0.99 |
| 241_S | 245_A | 1.340 | 0.99 |
| 118_F | 121_L | 1.331 | 0.99 |
| 25_F | 60_K | 1.327 | 0.99 |
| 136_F | 226_I | 1.325 | 0.99 |
| 343_E | 387_A | 1.295 | 0.99 |
| 73_A | 131_K | 1.295 | 0.99 |
| 253_F | 279_S | 1.292 | 0.99 |
| 53_D | 56_G | 1.286 | 0.99 |
| 343_E | 386_T | 1.282 | 0.99 |
| 245_A | 248_N | 1.279 | 0.99 |
| 210_Y | 214_A | 1.267 | 0.99 |
| 373_D | 376_A | 1.264 | 0.99 |
| 389_Q | 393_K | 1.263 | 0.99 |
| 131_K | 224_D | 1.262 | 0.99 |
| 246_V | 252_V | 1.256 | 0.99 |
| 15_D | 73_A | 1.255 | 0.99 |
| 257_E | 328_D | 1.255 | 0.99 |
| 138_P | 228_M | 1.253 | 0.99 |
| 58_I | 117_D | 1.252 | 0.99 |
| 134_I | 223_I | 1.247 | 0.99 |
| 71_V | 130_I | 1.228 | 0.98 |
| 144_A | 196_D | 1.225 | 0.98 |
| 243_M | 254_T | 1.225 | 0.98 |
| 395_A | 399_K | 1.223 | 0.98 |
| 229_D | 328_D | 1.212 | 0.98 |
| 299_N | 302_G | 1.202 | 0.98 |
| 243_M | 247_N | 1.199 | 0.98 |
| 102_A | 105_F | 1.191 | 0.98 |
| 385_T | 389_Q | 1.186 | 0.98 |
| 346_L | 362_T | 1.168 | 0.97 |
| 230_A | 233_H | 1.162 | 0.97 |
| 115_I | 119_Q | 1.161 | 0.97 |
| 247_N | 282_D | 1.161 | 0.97 |
| 105_F | 200_L | 1.159 | 0.97 |
| 69_M | 388_Y | 1.153 | 0.97 |
| 65_Y | 388_Y | 1.151 | 0.97 |
| 79_P | 108_T | 1.150 | 0.97 |
| 61_I | 64_G | 1.140 | 0.97 |
| 321_V | 357_A | 1.132 | 0.97 |
| 141_T | 162_T | 1.131 | 0.97 |
| 28_G | 53_D | 1.124 | 0.97 |
| 85_S | 196_D | 1.120 | 0.96 |
| 238_W | 242_F | 1.119 | 0.96 |
| 227_R | 328_D | 1.118 | 0.96 |
| 324_I | 362_T | 1.107 | 0.96 |
| 397_L | 401_N | 1.107 | 0.96 |
| 55_Q | 114_T | 1.103 | 0.96 |
| 138_P | 211_L | 1.103 | 0.96 |
| 229_D | 257_E | 1.099 | 0.96 |
| 285_F | 352_S | 1.098 | 0.96 |
| 20_I | 66_L | 1.091 | 0.96 |
| 125_A | 128_K | 1.088 | 0.96 |
| 339_R | 384_S | 1.070 | 0.95 |
| 108_T | 218_W | 1.070 | 0.95 |
| 158_Y | 161_G | 1.067 | 0.95 |
| 54_W | 118_F | 1.066 | 0.95 |
| 71_V | 358_I | 1.066 | 0.95 |
| 21_F | 77_S | 1.060 | 0.95 |
| 123_A | 126_H | 1.059 | 0.95 |
| 289_V | 345_A | 1.059 | 0.95 |
| 123_A | 222_G | 1.056 | 0.95 |
| 324_I | 349_T | 1.051 | 0.94 |
| 215_I | 226_I | 1.042 | 0.94 |
| 289_V | 348_F | 1.039 | 0.94 |
| 339_R | 343_E | 1.039 | 0.94 |
| 241_S | 244_A | 1.038 | 0.94 |
| 227_R | 257_E | 1.035 | 0.94 |
| 143_P | 196_D | 1.033 | 0.94 |
| 17_I | 133_I | 1.031 | 0.94 |
| 216_K | 220_D | 1.029 | 0.94 |
| 229_D | 327_H | 1.026 | 0.94 |
| 16_V | 399_K | 1.015 | 0.93 |
| 140_H | 327_H | 1.010 | 0.93 |
| 61_I | 124_A | 1.007 | 0.93 |
| 122_I | 221_L | 1.004 | 0.93 |
| 209_V | 245_A | 1.004 | 0.93 |
| 65_Y | 68_G | 1.003 | 0.93 |
| 87_I | 92_V | 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 | 0.9558 | 100 | 0.132 | Contact Map |
| 3bmvA | 1 | 0.9853 | 100 | 0.135 | Contact Map |
| 4jclA | 1 | 0.9853 | 100 | 0.135 | Contact Map |
| 1d3cA | 1 | 0.9877 | 100 | 0.137 | Contact Map |
| 1qhoA | 1 | 0.9705 | 100 | 0.137 | Contact Map |
| 1cygA | 1 | 0.9779 | 100 | 0.143 | Contact Map |
| 2wc7A | 1 | 0.9017 | 100 | 0.185 | Contact Map |
| 1j0hA | 2 | 0.9214 | 100 | 0.19 | Contact Map |
| 1ea9C | 2 | 0.9238 | 100 | 0.193 | Contact Map |
| 2z1kA | 4 | 0.8993 | 100 | 0.193 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)