| TR829-test |
| ID: | 1411227717 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 67 (67) | ||
| Sequences: | 263 (208.7) | ||
| Seq/Len: | 3.925 | ||
| Nf(neff/√len): | 25.5 |
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: 3.925).
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 |
| 2_R | 23_E | 3.428 | 1.00 |
| 44_N | 54_F | 2.356 | 1.00 |
| 2_R | 12_S | 2.253 | 1.00 |
| 41_A | 54_F | 2.196 | 1.00 |
| 23_E | 33_Q | 1.915 | 1.00 |
| 55_F | 60_K | 1.881 | 1.00 |
| 7_S | 52_G | 1.501 | 0.97 |
| 2_R | 25_Q | 1.356 | 0.95 |
| 25_Q | 33_Q | 1.352 | 0.95 |
| 24_I | 67_K | 1.351 | 0.95 |
| 36_G | 64_L | 1.349 | 0.94 |
| 13_I | 45_F | 1.336 | 0.94 |
| 52_G | 60_K | 1.326 | 0.94 |
| 22_L | 34_Y | 1.317 | 0.94 |
| 12_S | 23_E | 1.285 | 0.92 |
| 35_L | 66_R | 1.283 | 0.92 |
| 22_L | 35_L | 1.278 | 0.92 |
| 52_G | 56_D | 1.231 | 0.90 |
| 42_H | 46_M | 1.221 | 0.90 |
| 56_D | 60_K | 1.216 | 0.89 |
| 13_I | 62_K | 1.204 | 0.89 |
| 5_V | 13_I | 1.197 | 0.88 |
| 38_P | 41_A | 1.187 | 0.88 |
| 26_F | 52_G | 1.177 | 0.87 |
| 21_M | 47_S | 1.175 | 0.87 |
| 15_Y | 41_A | 1.169 | 0.87 |
| 14_G | 25_Q | 1.155 | 0.86 |
| 41_A | 63_F | 1.130 | 0.84 |
| 22_L | 59_I | 1.108 | 0.83 |
| 5_V | 14_G | 1.068 | 0.79 |
| 36_G | 66_R | 1.046 | 0.77 |
| 48_A | 55_F | 1.033 | 0.76 |
| 8_S | 52_G | 1.033 | 0.76 |
| 17_P | 30_G | 1.022 | 0.75 |
| 10_I | 55_F | 1.011 | 0.74 |
| 8_S | 32_Y | 1.002 | 0.73 |
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 | |
| 3nv7A | 1 | 0.5224 | 16 | 0.883 | Contact Map |
| 4khbD | 4 | 0.9552 | 13.8 | 0.886 | Contact Map |
| 2qmeI | 1 | 0.3433 | 13.4 | 0.887 | Contact Map |
| 4jpdA | 1 | 0.9701 | 11.8 | 0.89 | Contact Map |
| 4hs5A | 2 | 0.9701 | 11.2 | 0.89 | Contact Map |
| 2odbB | 1 | 0.5075 | 10.7 | 0.892 | Contact Map |
| 3k8rA | 2 | 0.8657 | 9.1 | 0.895 | Contact Map |
| 2x8nA | 1 | 0.9552 | 8.9 | 0.896 | Contact Map |
| 3nbkA | 4 | 0.5522 | 8.8 | 0.896 | Contact Map |
| 3fssA | 1 | 0.7761 | 8.5 | 0.896 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)