| knl1_es |
| ID: | 1490115881 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 42 (41) | ||
| Sequences: | 156 (120.8) | ||
| Seq/Len: | 3.805 | ||
| Nf(neff/√len): | 18.9 |
HHblits Results: (2016_02)
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: 3.805).
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 |
| 21_H | 38_E | 1.767 | 0.99 |
| 1_D | 6_K | 1.534 | 0.98 |
| 9_Y | 34_A | 1.529 | 0.98 |
| 21_H | 31_K | 1.512 | 0.97 |
| 14_Q | 41_L | 1.500 | 0.97 |
| 26_I | 37_Q | 1.442 | 0.96 |
| 3_L | 24_G | 1.320 | 0.93 |
| 17_E | 30_L | 1.289 | 0.92 |
| 22_A | 37_Q | 1.234 | 0.90 |
| 2_L | 5_D | 1.179 | 0.87 |
| 14_Q | 32_T | 1.159 | 0.85 |
| 27_I | 35_E | 1.143 | 0.84 |
| 32_T | 39_K | 1.134 | 0.84 |
| 17_E | 24_G | 1.125 | 0.83 |
| 22_A | 25_Q | 1.119 | 0.83 |
| 6_K | 12_K | 1.118 | 0.83 |
| 37_Q | 40_P | 1.116 | 0.82 |
| 2_L | 31_K | 1.105 | 0.82 |
| 5_D | 13_L | 1.101 | 0.81 |
| 19_E | 24_G | 1.093 | 0.81 |
| 4_L | 31_K | 1.070 | 0.79 |
| 13_L | 36_M | 1.039 | 0.76 |
| 24_G | 35_E | 1.034 | 0.75 |
| 28_Q | 32_T | 1.026 | 0.74 |
| 10_Q | 29_E | 1.022 | 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 | |
| 2beqD | 3 | 0.7857 | 5.2 | 0.806 | Contact Map |
| 3bqoA | 1 | 0.9762 | 5.1 | 0.807 | Contact Map |
| 4bt9A | 2 | 1 | 4.3 | 0.813 | Contact Map |
| 1ikpA | 1 | 1 | 3.9 | 0.817 | Contact Map |
| 1m1jA | 2 | 1 | 3.9 | 0.818 | Contact Map |
| 1slqA | 6 | 1 | 3.6 | 0.82 | Contact Map |
| 1fzcA | 2 | 0.381 | 3.6 | 0.82 | Contact Map |
| 3f4mA | 1 | 0.7381 | 3.4 | 0.822 | Contact Map |
| 1bf5A | 1 | 0.619 | 3.3 | 0.824 | Contact Map |
| 1s35A | 1 | 0.7143 | 3.2 | 0.824 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)