| SP17106A |
| ID: | 1395700868 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 159 (154) | ||
| Sequences: | 315 (260) | ||
| Seq/Len: | 2.045 | ||
| Nf(neff/√len): | 21.0 |
HHblits Results: (2013_03)
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: 2.045).
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 |
| 55_R | 81_E | 2.975 | 1.00 |
| 12_E | 157_T | 2.598 | 1.00 |
| 127_T | 130_P | 2.539 | 1.00 |
| 84_D | 132_Y | 2.482 | 1.00 |
| 14_L | 140_A | 2.438 | 1.00 |
| 76_T | 92_T | 2.397 | 1.00 |
| 125_F | 135_L | 2.220 | 1.00 |
| 48_E | 53_K | 2.195 | 1.00 |
| 86_A | 127_T | 2.106 | 0.99 |
| 16_K | 154_D | 2.082 | 0.99 |
| 82_T | 132_Y | 1.977 | 0.99 |
| 78_Y | 92_T | 1.908 | 0.99 |
| 37_R | 65_I | 1.682 | 0.96 |
| 86_A | 129_S | 1.664 | 0.96 |
| 82_T | 86_A | 1.651 | 0.95 |
| 92_T | 153_Y | 1.638 | 0.95 |
| 67_D | 73_I | 1.564 | 0.93 |
| 86_A | 128_S | 1.559 | 0.93 |
| 78_Y | 90_L | 1.483 | 0.91 |
| 76_T | 90_L | 1.433 | 0.89 |
| 77_R | 91_Q | 1.401 | 0.87 |
| 37_R | 126_E | 1.383 | 0.86 |
| 96_R | 146_R | 1.368 | 0.85 |
| 8_P | 158_L | 1.350 | 0.84 |
| 127_T | 131_K | 1.339 | 0.84 |
| 40_I | 64_Q | 1.326 | 0.83 |
| 63_W | 77_R | 1.319 | 0.83 |
| 98_G | 103_L | 1.313 | 0.82 |
| 79_L | 87_L | 1.291 | 0.81 |
| 122_T | 139_V | 1.281 | 0.80 |
| 84_D | 128_S | 1.281 | 0.80 |
| 84_D | 88_I | 1.268 | 0.79 |
| 19_V | 143_S | 1.262 | 0.79 |
| 61_A | 139_V | 1.252 | 0.78 |
| 42_I | 56_I | 1.248 | 0.77 |
| 64_Q | 92_T | 1.241 | 0.77 |
| 93_K | 124_Q | 1.239 | 0.77 |
| 106_L | 144_A | 1.231 | 0.76 |
| 92_T | 123_M | 1.198 | 0.73 |
| 102_T | 112_V | 1.197 | 0.73 |
| 22_N | 156_Y | 1.173 | 0.71 |
| 32_S | 105_Q | 1.164 | 0.70 |
| 100_A | 104_K | 1.147 | 0.69 |
| 13_P | 50_K | 1.130 | 0.67 |
| 92_T | 144_A | 1.119 | 0.66 |
| 92_T | 140_A | 1.117 | 0.66 |
| 92_T | 155_A | 1.117 | 0.66 |
| 123_M | 155_A | 1.114 | 0.65 |
| 138_T | 157_T | 1.109 | 0.65 |
| 47_F | 80_L | 1.105 | 0.64 |
| 38_R | 96_R | 1.102 | 0.64 |
| 135_L | 158_L | 1.102 | 0.64 |
| 13_P | 16_K | 1.101 | 0.64 |
| 14_L | 138_T | 1.100 | 0.64 |
| 20_D | 44_G | 1.095 | 0.63 |
| 29_G | 35_G | 1.062 | 0.60 |
| 29_G | 151_V | 1.059 | 0.59 |
| 74_I | 151_V | 1.056 | 0.59 |
| 75_D | 153_Y | 1.054 | 0.59 |
| 14_L | 157_T | 1.038 | 0.57 |
| 57_L | 77_R | 1.029 | 0.56 |
| 59_N | 119_F | 1.029 | 0.56 |
| 37_R | 49_G | 1.024 | 0.56 |
| 102_T | 117_Y | 1.022 | 0.55 |
| 42_I | 90_L | 1.010 | 0.54 |
| 17_F | 47_F | 1.010 | 0.54 |
| 147_L | 150_A | 1.003 | 0.53 |
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 | |
| 3g7gA | 8 | 0.9686 | 100 | 0.058 | Contact Map |
| 3c5oA | 4 | 0.956 | 100 | 0.068 | Contact Map |
| 2r5iA | 15 | 0.3585 | 6.8 | 0.95 | Contact Map |
| 3oaeA | 5 | 0.3019 | 5.7 | 0.951 | Contact Map |
| 1dzlA | 1 | 0.2893 | 5.4 | 0.952 | Contact Map |
| 1darA | 1 | 0.5849 | 3.4 | 0.957 | Contact Map |
| 1dp7P | 1 | 0.1824 | 3.4 | 0.957 | Contact Map |
| 3balA | 4 | 0.7107 | 3.2 | 0.957 | Contact Map |
| 1xvsA | 2 | 0.6415 | 3 | 0.958 | Contact Map |
| 2f1eA | 1 | 0.6164 | 2.9 | 0.958 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)