| Compound 3 |
| ID: | 1430781768 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 184 (179) | ||
| Sequences: | 640 (355.3) | ||
| Seq/Len: | 3.575 | ||
| Nf(neff/√len): | 26.6 |
Jackhmmer Results: (2015_01_07)
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: 3.575).
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 |
| 72_R | 118_D | 3.754 | 1.00 |
| 99_S | 147_N | 3.571 | 1.00 |
| 80_V | 145_F | 3.407 | 1.00 |
| 108_T | 125_T | 3.406 | 1.00 |
| 94_K | 157_M | 3.252 | 1.00 |
| 144_T | 147_N | 3.169 | 1.00 |
| 67_L | 143_I | 3.040 | 1.00 |
| 25_Y | 170_T | 2.980 | 1.00 |
| 129_S | 148_H | 2.733 | 1.00 |
| 57_W | 63_G | 2.576 | 1.00 |
| 146_S | 150_N | 2.488 | 1.00 |
| 105_D | 132_Q | 2.422 | 1.00 |
| 110_T | 125_T | 2.396 | 1.00 |
| 72_R | 164_A | 2.326 | 1.00 |
| 170_T | 179_S | 2.200 | 1.00 |
| 102_G | 133_S | 2.170 | 1.00 |
| 118_D | 122_T | 2.155 | 1.00 |
| 145_F | 149_V | 2.124 | 1.00 |
| 94_K | 108_T | 2.117 | 1.00 |
| 24_N | 180_N | 2.094 | 1.00 |
| 83_S | 136_P | 1.795 | 0.99 |
| 50_I | 166_Q | 1.728 | 0.99 |
| 99_S | 144_T | 1.633 | 0.98 |
| 103_T | 132_Q | 1.603 | 0.98 |
| 94_K | 125_T | 1.602 | 0.98 |
| 143_I | 168_M | 1.599 | 0.98 |
| 108_T | 157_M | 1.564 | 0.98 |
| 106_I | 155_H | 1.540 | 0.97 |
| 84_W | 88_R | 1.537 | 0.97 |
| 45_S | 166_Q | 1.537 | 0.97 |
| 55_G | 181_V | 1.517 | 0.97 |
| 36_V | 169_A | 1.513 | 0.97 |
| 76_I | 127_Y | 1.467 | 0.96 |
| 88_R | 105_D | 1.444 | 0.96 |
| 82_D | 143_I | 1.426 | 0.96 |
| 83_S | 134_K | 1.403 | 0.95 |
| 25_Y | 179_S | 1.399 | 0.95 |
| 106_I | 151_A | 1.389 | 0.95 |
| 6_L | 167_V | 1.386 | 0.95 |
| 102_G | 132_Q | 1.381 | 0.94 |
| 90_T | 107_Y | 1.364 | 0.94 |
| 81_V | 130_V | 1.359 | 0.94 |
| 153_K | 158_N | 1.353 | 0.94 |
| 27_V | 35_F | 1.350 | 0.94 |
| 20_G | 24_N | 1.325 | 0.93 |
| 49_T | 142_T | 1.316 | 0.92 |
| 50_I | 67_L | 1.313 | 0.92 |
| 27_V | 179_S | 1.296 | 0.92 |
| 54_A | 181_V | 1.290 | 0.91 |
| 109_T | 114_A | 1.247 | 0.89 |
| 7_N | 37_V | 1.243 | 0.89 |
| 67_L | 168_M | 1.221 | 0.88 |
| 147_N | 150_N | 1.213 | 0.88 |
| 93_Y | 105_D | 1.204 | 0.87 |
| 20_G | 180_N | 1.196 | 0.87 |
| 150_N | 154_S | 1.191 | 0.86 |
| 137_T | 181_V | 1.189 | 0.86 |
| 29_W | 177_G | 1.186 | 0.86 |
| 80_V | 149_V | 1.186 | 0.86 |
| 87_Y | 90_T | 1.155 | 0.84 |
| 116_S | 123_T | 1.108 | 0.80 |
| 3_D | 6_L | 1.102 | 0.80 |
| 84_W | 90_T | 1.102 | 0.80 |
| 112_Y | 125_T | 1.093 | 0.79 |
| 150_N | 153_K | 1.082 | 0.78 |
| 38_G | 41_W | 1.081 | 0.78 |
| 12_G | 32_T | 1.072 | 0.77 |
| 72_R | 122_T | 1.053 | 0.75 |
| 46_P | 146_S | 1.047 | 0.75 |
| 69_G | 152_W | 1.039 | 0.74 |
| 48_R | 166_Q | 1.039 | 0.74 |
| 9_T | 33_G | 1.036 | 0.74 |
| 103_T | 133_S | 1.026 | 0.73 |
| 93_Y | 107_Y | 1.021 | 0.72 |
| 17_A | 143_I | 1.019 | 0.72 |
| 16_N | 60_N | 1.017 | 0.72 |
| 50_I | 143_I | 1.012 | 0.71 |
| 32_T | 174_Q | 1.010 | 0.71 |
| 13_G | 32_T | 1.009 | 0.71 |
| 151_A | 155_H | 1.005 | 0.70 |
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 | |
| 2z79A | 2 | 1 | 100 | -0.038 | Contact Map |
| 1ynaA | 1 | 0.9674 | 100 | -0.008 | Contact Map |
| 3wp3A | 2 | 0.962 | 100 | -0.008 | Contact Map |
| 1axkA | 2 | 0.9946 | 100 | -0.006 | Contact Map |
| 3mf6A | 1 | 0.962 | 100 | -0.003 | Contact Map |
| 1xnkA | 2 | 0.9674 | 100 | -0.001 | Contact Map |
| 2vgdA | 1 | 0.962 | 100 | 0.014 | Contact Map |
| 1xynA | 1 | 0.9402 | 100 | 0.018 | Contact Map |
| 3m4fA | 4 | 0.9565 | 100 | 0.02 | Contact Map |
| 3akqA | 1 | 0.9674 | 100 | 0.02 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)