| 1WA3_AB |
| ID: | 1490808653 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 205 (201) | ||
| Sequences: | 3492 (2273.5) | ||
| Seq/Len: | 17.373 | ||
| Nf(neff/√len): | 160.4 |
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: 17.373).
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 |
| 56_S | 85_E | 3.655 | 1.00 |
| 94_E | 119_K | 2.677 | 1.00 |
| 80_V | 105_V | 2.558 | 1.00 |
| 50_T | 53_K | 2.464 | 1.00 |
| 93_D | 122_K | 2.448 | 1.00 |
| 29_L | 58_L | 2.387 | 1.00 |
| 28_A | 55_L | 2.315 | 1.00 |
| 30_A | 34_G | 2.285 | 1.00 |
| 72_S | 75_Q | 2.170 | 1.00 |
| 49_D | 78_K | 2.133 | 1.00 |
| 97_S | 107_Y | 2.103 | 1.00 |
| 53_K | 57_F | 1.968 | 1.00 |
| 43_F | 49_D | 1.965 | 1.00 |
| 98_Q | 123_L | 1.961 | 1.00 |
| 111_V | 128_L | 1.953 | 1.00 |
| 77_R | 99_F | 1.924 | 1.00 |
| 120_A | 128_L | 1.895 | 1.00 |
| 25_K | 58_L | 1.838 | 1.00 |
| 77_R | 81_E | 1.829 | 1.00 |
| 165_C | 169_K | 1.806 | 1.00 |
| 74_E | 78_K | 1.804 | 1.00 |
| 20_S | 23_E | 1.802 | 1.00 |
| 121_M | 151_V | 1.762 | 1.00 |
| 117_L | 151_V | 1.760 | 1.00 |
| 70_V | 87_I | 1.741 | 1.00 |
| 140_F | 144_M | 1.738 | 1.00 |
| 25_K | 54_E | 1.736 | 1.00 |
| 75_Q | 78_K | 1.721 | 1.00 |
| 52_I | 67_A | 1.694 | 1.00 |
| 99_F | 103_K | 1.693 | 1.00 |
| 87_I | 100_C | 1.688 | 1.00 |
| 190_R | 194_K | 1.667 | 1.00 |
| 100_C | 107_Y | 1.654 | 1.00 |
| 79_A | 84_A | 1.654 | 1.00 |
| 91_H | 118_V | 1.648 | 1.00 |
| 41_I | 55_L | 1.637 | 1.00 |
| 32_F | 63_A | 1.637 | 1.00 |
| 101_K | 126_T | 1.622 | 1.00 |
| 92_L | 123_L | 1.619 | 1.00 |
| 188_E | 191_E | 1.606 | 1.00 |
| 113_T | 116_E | 1.603 | 1.00 |
| 89_S | 107_Y | 1.595 | 1.00 |
| 92_L | 97_S | 1.591 | 1.00 |
| 47_D | 50_T | 1.552 | 1.00 |
| 111_V | 117_L | 1.549 | 1.00 |
| 33_E | 190_R | 1.533 | 1.00 |
| 141_V | 172_V | 1.527 | 1.00 |
| 21_V | 47_D | 1.518 | 1.00 |
| 29_L | 33_E | 1.506 | 1.00 |
| 136_V | 140_F | 1.499 | 1.00 |
| 76_C | 87_I | 1.459 | 1.00 |
| 13_V | 154_V | 1.453 | 1.00 |
| 121_M | 150_N | 1.437 | 1.00 |
| 186_P | 192_K | 1.416 | 1.00 |
| 76_C | 99_F | 1.412 | 1.00 |
| 66_G | 86_F | 1.411 | 1.00 |
| 77_R | 103_K | 1.407 | 0.99 |
| 95_E | 122_K | 1.394 | 0.99 |
| 16_L | 39_I | 1.363 | 0.99 |
| 114_P | 144_M | 1.359 | 0.99 |
| 112_M | 136_V | 1.344 | 0.99 |
| 92_L | 111_V | 1.341 | 0.99 |
| 99_F | 102_E | 1.338 | 0.99 |
| 134_E | 139_Q | 1.313 | 0.99 |
| 191_E | 195_A | 1.302 | 0.99 |
| 160_N | 163_N | 1.291 | 0.99 |
| 28_A | 39_I | 1.287 | 0.99 |
| 188_E | 192_K | 1.285 | 0.99 |
| 130_L | 153_F | 1.263 | 0.99 |
| 71_T | 75_Q | 1.256 | 0.99 |
| 43_F | 79_A | 1.251 | 0.99 |
| 133_G | 159_V | 1.248 | 0.99 |
| 118_V | 148_F | 1.245 | 0.98 |
| 52_I | 65_I | 1.234 | 0.98 |
| 94_E | 123_L | 1.231 | 0.98 |
| 194_K | 198_E | 1.230 | 0.98 |
| 76_C | 96_I | 1.217 | 0.98 |
| 50_T | 54_E | 1.210 | 0.98 |
| 89_S | 109_P | 1.205 | 0.98 |
| 5_E | 8_K | 1.204 | 0.98 |
| 130_L | 136_V | 1.186 | 0.98 |
| 112_M | 140_F | 1.165 | 0.97 |
| 94_E | 98_Q | 1.157 | 0.97 |
| 88_V | 108_M | 1.154 | 0.97 |
| 117_L | 144_M | 1.151 | 0.97 |
| 164_V | 175_V | 1.149 | 0.97 |
| 98_Q | 102_E | 1.149 | 0.97 |
| 135_V | 140_F | 1.145 | 0.97 |
| 8_K | 152_K | 1.128 | 0.97 |
| 155_P | 172_V | 1.127 | 0.97 |
| 80_V | 103_K | 1.101 | 0.96 |
| 53_K | 81_E | 1.097 | 0.96 |
| 187_D | 191_E | 1.085 | 0.96 |
| 76_C | 100_C | 1.069 | 0.95 |
| 134_E | 143_A | 1.067 | 0.95 |
| 25_K | 29_L | 1.067 | 0.95 |
| 163_N | 166_E | 1.064 | 0.95 |
| 166_E | 169_K | 1.058 | 0.95 |
| 87_I | 105_V | 1.054 | 0.95 |
| 54_E | 58_L | 1.050 | 0.94 |
| 73_V | 95_E | 1.040 | 0.94 |
| 32_F | 37_H | 1.037 | 0.94 |
| 29_L | 59_K | 1.037 | 0.94 |
| 117_L | 148_F | 1.034 | 0.94 |
| 18_A | 51_V | 1.030 | 0.94 |
| 95_E | 98_Q | 1.030 | 0.94 |
| 107_Y | 125_H | 1.029 | 0.94 |
| 134_E | 167_W | 1.026 | 0.94 |
| 74_E | 77_R | 1.026 | 0.94 |
| 73_V | 99_F | 1.014 | 0.93 |
| 34_G | 190_R | 1.006 | 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 | |
| 4bk9A | 3 | 0.9854 | 100 | 0.458 | Contact Map |
| 1vhcA | 6 | 0.9805 | 100 | 0.459 | Contact Map |
| 3vcrA | 2 | 0.9805 | 100 | 0.463 | Contact Map |
| 2yw3A | 6 | 0.961 | 100 | 0.47 | Contact Map |
| 1wbhA | 3 | 0.9805 | 100 | 0.471 | Contact Map |
| 1mxsA | 1 | 0.9854 | 100 | 0.478 | Contact Map |
| 1wa3A | 6 | 0.9902 | 100 | 0.489 | Contact Map |
| 4e38A | 3 | 0.9805 | 100 | 0.504 | Contact Map |
| 2v82A | 1 | 0.9805 | 100 | 0.563 | Contact Map |
| 4qccA | 2 | 0.9659 | 100 | 0.565 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)