| 1sbp |
| ID: | 1482007836 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 329 (268) | ||
| Sequences: | 15968 (9897.7) | ||
| Seq/Len: | 59.582 | ||
| Nf(neff/√len): | 604.6 |
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: 59.582).
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 |
| 23_Q | 58_R | 4.036 | 1.00 |
| 122_K | 228_E | 3.689 | 1.00 |
| 98_D | 255_K | 3.284 | 1.00 |
| 123_G | 226_K | 3.122 | 1.00 |
| 42_A | 264_Y | 2.992 | 1.00 |
| 176_D | 180_A | 2.975 | 1.00 |
| 37_E | 41_K | 2.898 | 1.00 |
| 25_L | 58_R | 2.896 | 1.00 |
| 53_D | 257_V | 2.856 | 1.00 |
| 23_Q | 54_N | 2.843 | 1.00 |
| 47_W | 51_T | 2.808 | 1.00 |
| 267_S | 270_G | 2.780 | 1.00 |
| 44_S | 54_N | 2.614 | 1.00 |
| 47_W | 260_A | 2.600 | 1.00 |
| 120_V | 228_E | 2.565 | 1.00 |
| 42_A | 45_A | 2.526 | 1.00 |
| 260_A | 263_K | 2.520 | 1.00 |
| 179_K | 183_K | 2.519 | 1.00 |
| 130_D | 133_D | 2.466 | 1.00 |
| 43_F | 260_A | 2.362 | 1.00 |
| 78_D | 254_T | 2.340 | 1.00 |
| 38_Q | 41_K | 2.320 | 1.00 |
| 135_I | 180_A | 2.253 | 1.00 |
| 40_N | 261_Y | 2.219 | 1.00 |
| 41_K | 45_A | 2.205 | 1.00 |
| 21_D | 54_N | 2.134 | 1.00 |
| 42_A | 273_I | 2.130 | 1.00 |
| 180_A | 184_N | 2.106 | 1.00 |
| 133_D | 136_K | 2.045 | 1.00 |
| 255_K | 259_E | 2.017 | 1.00 |
| 268_P | 272_E | 2.017 | 1.00 |
| 22_I | 257_V | 2.015 | 1.00 |
| 139_V | 184_N | 1.995 | 1.00 |
| 244_V | 258_A | 1.975 | 1.00 |
| 272_E | 276_K | 1.969 | 1.00 |
| 40_N | 44_S | 1.952 | 1.00 |
| 125_P | 207_V | 1.899 | 1.00 |
| 97_I | 243_S | 1.896 | 1.00 |
| 25_L | 60_S | 1.873 | 1.00 |
| 173_K | 176_D | 1.870 | 1.00 |
| 124_N | 206_D | 1.850 | 1.00 |
| 120_V | 230_V | 1.814 | 1.00 |
| 41_K | 44_S | 1.791 | 1.00 |
| 254_T | 257_V | 1.753 | 1.00 |
| 98_D | 246_D | 1.730 | 1.00 |
| 42_A | 46_H | 1.728 | 1.00 |
| 80_V | 245_V | 1.715 | 1.00 |
| 172_A | 176_D | 1.708 | 1.00 |
| 122_K | 226_K | 1.707 | 1.00 |
| 256_A | 260_A | 1.689 | 1.00 |
| 43_F | 53_D | 1.674 | 1.00 |
| 47_W | 52_G | 1.658 | 1.00 |
| 244_V | 262_L | 1.649 | 1.00 |
| 22_I | 254_T | 1.648 | 1.00 |
| 177_F | 180_A | 1.630 | 1.00 |
| 33_R | 37_E | 1.627 | 1.00 |
| 117_V | 229_I | 1.608 | 1.00 |
| 256_A | 259_E | 1.602 | 1.00 |
| 108_N | 241_T | 1.576 | 1.00 |
| 199_F | 205_G | 1.557 | 1.00 |
| 43_F | 261_Y | 1.548 | 1.00 |
| 270_G | 273_I | 1.545 | 1.00 |
| 129_H | 133_D | 1.542 | 1.00 |
| 259_E | 263_K | 1.538 | 1.00 |
| 122_K | 126_K | 1.531 | 1.00 |
| 136_K | 139_V | 1.526 | 1.00 |
| 121_R | 124_N | 1.518 | 1.00 |
| 79_V | 258_A | 1.515 | 1.00 |
| 273_I | 276_K | 1.498 | 1.00 |
| 268_P | 285_D | 1.485 | 1.00 |
| 132_N | 135_I | 1.478 | 1.00 |
| 118_F | 230_V | 1.469 | 1.00 |
| 92_A | 107_D | 1.465 | 1.00 |
| 199_F | 204_I | 1.465 | 1.00 |
| 54_N | 58_R | 1.458 | 1.00 |
| 43_F | 264_Y | 1.458 | 1.00 |
| 272_E | 286_V | 1.457 | 1.00 |
| 44_S | 51_T | 1.455 | 1.00 |
| 21_D | 52_G | 1.425 | 1.00 |
| 66_K | 69_T | 1.416 | 1.00 |
| 38_Q | 42_A | 1.412 | 1.00 |
| 53_D | 260_A | 1.410 | 1.00 |
| 261_Y | 265_L | 1.404 | 0.99 |
| 40_N | 57_I | 1.388 | 0.99 |
| 198_T | 202_R | 1.375 | 0.99 |
| 40_N | 59_Q | 1.366 | 0.99 |
| 42_A | 269_E | 1.360 | 0.99 |
| 132_N | 136_K | 1.357 | 0.99 |
| 135_I | 181_L | 1.355 | 0.99 |
| 46_H | 269_E | 1.349 | 0.99 |
| 135_I | 139_V | 1.344 | 0.99 |
| 269_E | 272_E | 1.343 | 0.99 |
| 129_H | 233_S | 1.342 | 0.99 |
| 268_P | 283_D | 1.339 | 0.99 |
| 248_V | 254_T | 1.333 | 0.99 |
| 176_D | 179_K | 1.331 | 0.99 |
| 257_V | 260_A | 1.319 | 0.99 |
| 118_F | 207_V | 1.315 | 0.99 |
| 79_V | 261_Y | 1.313 | 0.99 |
| 63_G | 66_K | 1.284 | 0.99 |
| 28_S | 59_Q | 1.279 | 0.99 |
| 191_G | 195_S | 1.278 | 0.99 |
| 128_I | 133_D | 1.268 | 0.99 |
| 180_A | 183_K | 1.253 | 0.99 |
| 38_Q | 273_I | 1.252 | 0.99 |
| 248_V | 255_K | 1.241 | 0.98 |
| 135_I | 184_N | 1.236 | 0.98 |
| 43_F | 257_V | 1.218 | 0.98 |
| 95_G | 246_D | 1.189 | 0.98 |
| 177_F | 181_L | 1.188 | 0.98 |
| 136_K | 140_S | 1.178 | 0.98 |
| 119_L | 210_A | 1.176 | 0.98 |
| 242_V | 262_L | 1.172 | 0.98 |
| 264_Y | 270_G | 1.160 | 0.97 |
| 82_L | 243_S | 1.159 | 0.97 |
| 246_D | 255_K | 1.154 | 0.97 |
| 46_H | 51_T | 1.149 | 0.97 |
| 71_V | 80_V | 1.142 | 0.97 |
| 24_L | 257_V | 1.115 | 0.96 |
| 26_N | 242_V | 1.109 | 0.96 |
| 272_E | 289_K | 1.106 | 0.96 |
| 39_Y | 264_Y | 1.090 | 0.96 |
| 27_V | 77_A | 1.089 | 0.96 |
| 34_E | 38_Q | 1.084 | 0.96 |
| 39_Y | 270_G | 1.084 | 0.96 |
| 79_V | 262_L | 1.063 | 0.95 |
| 24_L | 261_Y | 1.062 | 0.95 |
| 51_T | 260_A | 1.056 | 0.95 |
| 22_I | 53_D | 1.055 | 0.95 |
| 72_I | 94_R | 1.052 | 0.95 |
| 244_V | 259_E | 1.042 | 0.94 |
| 244_V | 248_V | 1.038 | 0.94 |
| 80_V | 243_S | 1.028 | 0.94 |
| 137_P | 207_V | 1.027 | 0.94 |
| 42_A | 270_G | 1.016 | 0.93 |
| 162_Y | 173_K | 1.015 | 0.93 |
| 43_F | 47_W | 1.014 | 0.93 |
| 34_E | 37_E | 1.012 | 0.93 |
| 135_I | 177_F | 1.009 | 0.93 |
| 125_P | 137_P | 1.004 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3waeA | 2 | 0.8541 | 100 | 0.44 | Contact Map |
| 4edpA | 2 | 0.8693 | 100 | 0.449 | Contact Map |
| 1sbpA | 1 | 0.924 | 100 | 0.453 | Contact Map |
| 3rpwA | 1 | 0.8571 | 100 | 0.46 | Contact Map |
| 3uorA | 2 | 0.8997 | 100 | 0.463 | Contact Map |
| 3c9hA | 2 | 0.8815 | 100 | 0.48 | Contact Map |
| 4mfiA | 1 | 0.8967 | 100 | 0.482 | Contact Map |
| 4r9fA | 1 | 0.8906 | 100 | 0.482 | Contact Map |
| 3pu5A | 1 | 0.8784 | 100 | 0.483 | Contact Map |
| 4eqbA | 2 | 0.8693 | 100 | 0.484 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)