| TPR-BUBs 8-147 |
| ID: | 1455705720 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 140 (136) | ||
| Sequences: | 547 (367.1) | ||
| Seq/Len: | 4.022 | ||
| Nf(neff/√len): | 31.5 |
HHblits Results: (2015_06)
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: 4.022).
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 |
| 103_E | 139_R | 4.322 | 1.00 |
| 96_E | 128_R | 2.835 | 1.00 |
| 136_F | 139_R | 2.815 | 1.00 |
| 45_C | 64_I | 2.548 | 1.00 |
| 25_T | 41_L | 2.471 | 1.00 |
| 16_E | 20_R | 2.386 | 1.00 |
| 22_I | 64_I | 2.321 | 1.00 |
| 62_L | 82_L | 2.090 | 1.00 |
| 26_E | 67_K | 2.069 | 1.00 |
| 118_G | 129_L | 1.999 | 1.00 |
| 55_Y | 58_D | 1.837 | 1.00 |
| 55_Y | 60_R | 1.790 | 0.99 |
| 117_R | 121_M | 1.786 | 0.99 |
| 115_Y | 136_F | 1.636 | 0.99 |
| 61_Y | 65_W | 1.608 | 0.99 |
| 107_A | 110_Q | 1.606 | 0.99 |
| 59_V | 91_H | 1.566 | 0.98 |
| 5_A | 17_V | 1.511 | 0.98 |
| 22_I | 45_C | 1.472 | 0.97 |
| 49_L | 61_Y | 1.453 | 0.97 |
| 49_L | 55_Y | 1.443 | 0.97 |
| 25_T | 29_F | 1.433 | 0.97 |
| 13_D | 60_R | 1.432 | 0.97 |
| 112_G | 133_L | 1.431 | 0.97 |
| 27_Q | 67_K | 1.429 | 0.97 |
| 112_G | 116_D | 1.375 | 0.95 |
| 11_G | 18_W | 1.334 | 0.94 |
| 86_D | 89_Q | 1.302 | 0.93 |
| 18_W | 45_C | 1.298 | 0.93 |
| 132_K | 135_Q | 1.274 | 0.92 |
| 29_F | 36_T | 1.256 | 0.92 |
| 103_E | 115_Y | 1.233 | 0.91 |
| 46_T | 64_I | 1.223 | 0.90 |
| 69_A | 91_H | 1.221 | 0.90 |
| 119_I | 126_T | 1.218 | 0.90 |
| 122_R | 126_T | 1.193 | 0.89 |
| 14_P | 60_R | 1.189 | 0.88 |
| 94_F | 98_Y | 1.156 | 0.86 |
| 19_V | 64_I | 1.146 | 0.86 |
| 43_E | 68_Y | 1.146 | 0.86 |
| 62_L | 91_H | 1.136 | 0.85 |
| 12_D | 15_L | 1.135 | 0.85 |
| 98_Y | 114_V | 1.107 | 0.83 |
| 136_F | 140_M | 1.104 | 0.83 |
| 49_L | 60_R | 1.097 | 0.82 |
| 21_F | 44_R | 1.084 | 0.81 |
| 98_Y | 107_A | 1.080 | 0.81 |
| 62_L | 123_A | 1.075 | 0.80 |
| 122_R | 130_K | 1.067 | 0.80 |
| 119_I | 129_L | 1.062 | 0.79 |
| 133_L | 136_F | 1.058 | 0.79 |
| 21_F | 24_W | 1.057 | 0.79 |
| 61_Y | 88_G | 1.056 | 0.79 |
| 74_E | 105_R | 1.055 | 0.79 |
| 41_L | 106_G | 1.043 | 0.78 |
| 113_E | 117_R | 1.034 | 0.77 |
| 13_D | 58_D | 1.033 | 0.77 |
| 72_C | 78_I | 1.030 | 0.76 |
| 58_D | 111_A | 1.022 | 0.76 |
| 53_P | 56_R | 1.018 | 0.75 |
| 79_F | 134_A | 1.009 | 0.74 |
| 57_D | 89_Q | 1.007 | 0.74 |
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 | |
| 2wviA | 1 | 0.9714 | 100 | -0.01 | Contact Map |
| 3eslA | 2 | 1 | 100 | 0.006 | Contact Map |
| 4a1gA | 4 | 0.9857 | 100 | 0.018 | Contact Map |
| 4aezC | 3 | 1 | 100 | 0.116 | Contact Map |
| 4b94A | 4 | 0.9 | 99.8 | 0.565 | Contact Map |
| 4h7yA | 4 | 0.9 | 99.7 | 0.612 | Contact Map |
| 2ondA | 2 | 0.8714 | 97.9 | 0.813 | Contact Map |
| 2ooeA | 1 | 0.9143 | 97.4 | 0.83 | Contact Map |
| 2uy1A | 1 | 0.8143 | 94.3 | 0.872 | Contact Map |
| 4e6hA | 1 | 0.8714 | 88.8 | 0.89 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)