| 1BRS |
| ID: | 1429443093 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 90 (89) | ||
| Sequences: | 432 (333.8) | ||
| Seq/Len: | 4.854 | ||
| Nf(neff/√len): | 35.4 |
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: 4.854).
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 |
| 18_H | 31_Y | 4.493 | 1.00 |
| 13_S | 16_D | 2.199 | 1.00 |
| 19_Q | 33_E | 1.870 | 1.00 |
| 9_E | 56_Q | 1.796 | 1.00 |
| 34_N | 37_A | 1.777 | 1.00 |
| 27_L | 41_C | 1.687 | 0.99 |
| 38_L | 42_L | 1.610 | 0.99 |
| 17_L | 21_L | 1.581 | 0.99 |
| 28_P | 41_C | 1.576 | 0.99 |
| 8_G | 54_W | 1.541 | 0.99 |
| 32_G | 37_A | 1.518 | 0.99 |
| 35_L | 70_S | 1.485 | 0.98 |
| 52_L | 75_F | 1.478 | 0.98 |
| 17_L | 35_L | 1.456 | 0.98 |
| 22_K | 33_E | 1.449 | 0.98 |
| 11_I | 17_L | 1.419 | 0.97 |
| 60_S | 65_E | 1.395 | 0.97 |
| 39_W | 43_T | 1.381 | 0.97 |
| 14_I | 18_H | 1.336 | 0.96 |
| 38_L | 74_V | 1.310 | 0.95 |
| 32_G | 40_D | 1.279 | 0.95 |
| 48_Y | 82_G | 1.270 | 0.94 |
| 64_T | 67_G | 1.254 | 0.94 |
| 39_W | 74_V | 1.244 | 0.94 |
| 8_G | 20_T | 1.226 | 0.93 |
| 17_L | 71_V | 1.226 | 0.93 |
| 35_L | 38_L | 1.218 | 0.93 |
| 52_L | 59_Q | 1.211 | 0.92 |
| 30_Y | 41_C | 1.201 | 0.92 |
| 57_F | 68_A | 1.189 | 0.91 |
| 8_G | 56_Q | 1.184 | 0.91 |
| 43_T | 69_E | 1.167 | 0.90 |
| 41_C | 45_W | 1.160 | 0.90 |
| 43_T | 78_A | 1.154 | 0.90 |
| 35_L | 71_V | 1.142 | 0.89 |
| 42_L | 74_V | 1.120 | 0.88 |
| 21_L | 25_L | 1.111 | 0.87 |
| 54_W | 60_S | 1.097 | 0.86 |
| 47_E | 50_L | 1.076 | 0.85 |
| 49_P | 54_W | 1.061 | 0.84 |
| 86_T | 89_L | 1.053 | 0.83 |
| 7_N | 56_Q | 1.030 | 0.81 |
| 49_P | 75_F | 1.029 | 0.81 |
| 18_H | 41_C | 1.016 | 0.80 |
| 25_L | 46_V | 1.011 | 0.79 |
| 27_L | 38_L | 1.009 | 0.79 |
| 73_Q | 77_E | 1.007 | 0.79 |
| 34_N | 40_D | 1.001 | 0.78 |
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 | |
| 2za4B | 2 | 0.9889 | 99.9 | 0.052 | Contact Map |
| 2cx6A | 2 | 0.9556 | 99.9 | 0.165 | Contact Map |
| 1w5sA | 2 | 1 | 65.2 | 0.851 | Contact Map |
| 1fnnA | 2 | 0.9667 | 43 | 0.87 | Contact Map |
| 3te6A | 2 | 0.9222 | 23.8 | 0.886 | Contact Map |
| 2fnaA | 2 | 0.9444 | 22.8 | 0.887 | Contact Map |
| 1wvvA | 2 | 0.3889 | 20.5 | 0.889 | Contact Map |
| 2cjlA | 2 | 0.3889 | 19 | 0.891 | Contact Map |
| 2x5fA | 2 | 1 | 18.1 | 0.892 | Contact Map |
| 3hbeX | 1 | 0.3889 | 17.7 | 0.893 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)