| T0808 1-150 -force run |
| ID: | 1405031116 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 150 (145) | ||
| Sequences: | 77 (68.2) | ||
| Seq/Len: | 0.531 | ||
| Nf(neff/√len): | 5.7 |
Jackhmmer Results: (2014_04_16)
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: 0.531).
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 |
| 61_F | 117_I | 2.713 | 0.98 |
| 25_V | 57_V | 2.604 | 0.98 |
| 34_T | 58_S | 1.964 | 0.86 |
| 90_F | 107_I | 1.850 | 0.81 |
| 62_Y | 132_I | 1.779 | 0.77 |
| 121_G | 129_F | 1.701 | 0.72 |
| 58_S | 118_D | 1.664 | 0.70 |
| 69_A | 146_Y | 1.583 | 0.64 |
| 69_A | 139_N | 1.513 | 0.59 |
| 25_V | 102_V | 1.500 | 0.58 |
| 58_S | 116_R | 1.479 | 0.56 |
| 58_S | 120_Q | 1.444 | 0.54 |
| 58_S | 61_F | 1.430 | 0.53 |
| 20_P | 117_I | 1.426 | 0.52 |
| 61_F | 137_A | 1.409 | 0.51 |
| 75_A | 94_L | 1.398 | 0.50 |
| 33_V | 99_F | 1.394 | 0.50 |
| 109_I | 112_A | 1.391 | 0.50 |
| 34_T | 47_V | 1.385 | 0.49 |
| 79_S | 121_G | 1.368 | 0.48 |
| 82_K | 89_G | 1.364 | 0.48 |
| 34_T | 120_Q | 1.314 | 0.44 |
| 63_L | 117_I | 1.306 | 0.43 |
| 66_P | 146_Y | 1.299 | 0.42 |
| 18_A | 71_L | 1.286 | 0.41 |
| 32_Y | 139_N | 1.252 | 0.39 |
| 51_T | 64_H | 1.247 | 0.39 |
| 52_N | 60_Y | 1.245 | 0.38 |
| 145_N | 149_D | 1.241 | 0.38 |
| 25_V | 82_K | 1.231 | 0.37 |
| 125_S | 130_G | 1.230 | 0.37 |
| 67_T | 139_N | 1.225 | 0.37 |
| 32_Y | 58_S | 1.222 | 0.37 |
| 56_I | 120_Q | 1.216 | 0.36 |
| 90_F | 149_D | 1.206 | 0.36 |
| 25_V | 66_P | 1.200 | 0.35 |
| 125_S | 149_D | 1.199 | 0.35 |
| 26_G | 149_D | 1.189 | 0.34 |
| 94_L | 146_Y | 1.175 | 0.33 |
| 25_V | 119_L | 1.170 | 0.33 |
| 110_R | 132_I | 1.165 | 0.33 |
| 34_T | 118_D | 1.156 | 0.32 |
| 53_P | 130_G | 1.149 | 0.32 |
| 77_G | 130_G | 1.146 | 0.31 |
| 63_L | 94_L | 1.135 | 0.31 |
| 30_N | 121_G | 1.127 | 0.30 |
| 10_L | 15_T | 1.126 | 0.30 |
| 45_R | 128_G | 1.122 | 0.30 |
| 92_V | 132_I | 1.110 | 0.29 |
| 9_A | 13_C | 1.104 | 0.29 |
| 22_Q | 25_V | 1.099 | 0.28 |
| 63_L | 66_P | 1.098 | 0.28 |
| 26_G | 69_A | 1.082 | 0.27 |
| 83_V | 117_I | 1.080 | 0.27 |
| 58_S | 115_V | 1.075 | 0.27 |
| 83_V | 118_D | 1.075 | 0.27 |
| 106_S | 148_K | 1.071 | 0.27 |
| 68_T | 146_Y | 1.070 | 0.26 |
| 30_N | 59_I | 1.066 | 0.26 |
| 33_V | 147_V | 1.065 | 0.26 |
| 60_Y | 111_Q | 1.062 | 0.26 |
| 31_G | 135_L | 1.059 | 0.26 |
| 54_K | 57_V | 1.051 | 0.25 |
| 25_V | 63_L | 1.050 | 0.25 |
| 61_F | 118_D | 1.038 | 0.25 |
| 42_I | 121_G | 1.036 | 0.24 |
| 71_L | 136_I | 1.034 | 0.24 |
| 29_G | 132_I | 1.030 | 0.24 |
| 43_T | 81_I | 1.025 | 0.24 |
| 76_K | 136_I | 1.020 | 0.24 |
| 73_L | 94_L | 1.019 | 0.23 |
| 102_V | 135_L | 1.018 | 0.23 |
| 47_V | 120_Q | 1.014 | 0.23 |
| 71_L | 118_D | 1.008 | 0.23 |
| 26_G | 90_F | 1.007 | 0.23 |
| 119_L | 130_G | 1.001 | 0.22 |
| 35_R | 112_A | 1.000 | 0.22 |
| 52_N | 147_V | 1.000 | 0.22 |
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 | |
| 2bgoA | 1 | 0.72 | 96.5 | 0.854 | Contact Map |
| 3zm8A | 1 | 0.86 | 94.2 | 0.875 | Contact Map |
| 4kmqA | 1 | 0.84 | 91 | 0.888 | Contact Map |
| 2vzpA | 2 | 0.7733 | 89.9 | 0.89 | Contact Map |
| 2w87A | 2 | 0.84 | 89.8 | 0.89 | Contact Map |
| 2vzsA | 2 | 0.1733 | 88.4 | 0.893 | Contact Map |
| 2w47A | 1 | 0.8267 | 88.2 | 0.894 | Contact Map |
| 2w3jA | 1 | 0.8467 | 83.3 | 0.901 | Contact Map |
| 2wz8A | 1 | 0.7533 | 79 | 0.905 | Contact Map |
| 2cdpA | 4 | 0.8267 | 70.9 | 0.911 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)