| 1d1lhb |
| ID: | 1478900693 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 61 (60) | ||
| Sequences: | 95 (70.4) | ||
| Seq/Len: | 1.583 | ||
| Nf(neff/√len): | 9.1 |
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: 1.583).
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 |
| 25_V | 30_I | 2.300 | 0.99 |
| 25_V | 40_I | 1.990 | 0.98 |
| 11_A | 30_I | 1.931 | 0.98 |
| 10_Y | 19_T | 1.747 | 0.95 |
| 33_A | 58_W | 1.713 | 0.94 |
| 32_K | 42_L | 1.684 | 0.94 |
| 19_T | 42_L | 1.682 | 0.94 |
| 27_Q | 31_N | 1.631 | 0.92 |
| 45_N | 51_Y | 1.542 | 0.89 |
| 10_Y | 42_L | 1.458 | 0.85 |
| 11_A | 34_I | 1.455 | 0.85 |
| 32_K | 58_W | 1.417 | 0.83 |
| 26_Y | 29_A | 1.342 | 0.78 |
| 2_E | 34_I | 1.230 | 0.69 |
| 15_G | 55_V | 1.212 | 0.67 |
| 11_A | 33_A | 1.209 | 0.67 |
| 7_L | 55_V | 1.157 | 0.62 |
| 5_I | 44_I | 1.156 | 0.62 |
| 28_S | 44_I | 1.123 | 0.58 |
| 25_V | 28_S | 1.120 | 0.58 |
| 43_T | 46_A | 1.111 | 0.57 |
| 19_T | 58_W | 1.109 | 0.57 |
| 19_T | 33_A | 1.106 | 0.57 |
| 11_A | 58_W | 1.098 | 0.56 |
| 19_T | 32_K | 1.066 | 0.52 |
| 29_A | 37_G | 1.061 | 0.52 |
| 34_I | 46_A | 1.057 | 0.52 |
| 42_L | 58_W | 1.047 | 0.50 |
| 8_K | 56_K | 1.035 | 0.49 |
| 4_R | 41_F | 1.029 | 0.49 |
| 8_K | 46_A | 1.017 | 0.47 |
| 15_G | 53_E | 1.010 | 0.47 |
| 23_L | 50_V | 1.005 | 0.46 |
| 9_D | 50_V | 1.003 | 0.46 |
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 | |
| 2cw1A | 1 | 0.9836 | 99.7 | 0.378 | Contact Map |
| 2ovgA | 1 | 0.9508 | 98.9 | 0.582 | Contact Map |
| 2pijA | 2 | 0.9672 | 98.2 | 0.667 | Contact Map |
| 2hinA | 2 | 0.918 | 95.2 | 0.78 | Contact Map |
| 3fzvA | 4 | 0.8689 | 93.3 | 0.799 | Contact Map |
| 2esnA | 4 | 0.9344 | 92.7 | 0.803 | Contact Map |
| 3hhgA | 8 | 0.9672 | 92.6 | 0.803 | Contact Map |
| 1uthA | 1 | 0 | 91.9 | 0.807 | Contact Map |
| 3fxqA | 2 | 0.9672 | 91.4 | 0.81 | Contact Map |
| 1al3A | 1 | 0 | 91.2 | 0.811 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)