| ss |
| ID: | 1449679195 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (56) | ||
| Sequences: | 503 (503) | ||
| Seq/Len: | 8.982 | ||
| Nf(neff/√len): | 67.2 |
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: 8.982).
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 |
| 42_V | 54_P | 2.218 | 1.00 |
| 16_F | 33_Y | 1.495 | 1.00 |
| 8_N | 52_A | 1.470 | 1.00 |
| 2_E | 24_Y | 1.445 | 0.99 |
| 28_A | 52_A | 1.441 | 0.99 |
| 11_H | 51_P | 1.389 | 0.99 |
| 20_G | 24_Y | 1.364 | 0.99 |
| 5_G | 25_N | 1.336 | 0.99 |
| 29_L | 50_Q | 1.271 | 0.98 |
| 14_G | 38_D | 1.205 | 0.98 |
| 7_E | 28_A | 1.200 | 0.97 |
| 14_G | 17_P | 1.163 | 0.97 |
| 4_M | 10_A | 1.159 | 0.97 |
| 15_I | 50_Q | 1.147 | 0.96 |
| 6_D | 43_N | 1.138 | 0.96 |
| 8_N | 49_A | 1.132 | 0.96 |
| 8_N | 34_D | 1.119 | 0.96 |
| 6_D | 54_P | 1.113 | 0.95 |
| 32_L | 37_K | 1.093 | 0.95 |
| 15_I | 23_S | 1.090 | 0.95 |
| 30_G | 45_V | 1.085 | 0.95 |
| 36_A | 54_P | 1.085 | 0.95 |
| 10_A | 52_A | 1.085 | 0.95 |
| 32_L | 52_A | 1.082 | 0.95 |
| 26_D | 50_Q | 1.078 | 0.94 |
| 7_E | 18_H | 1.055 | 0.93 |
| 21_G | 45_V | 1.024 | 0.92 |
| 18_H | 51_P | 1.018 | 0.92 |
| 14_G | 49_A | 1.017 | 0.92 |
| 23_S | 40_G | 1.016 | 0.92 |
| 36_A | 44_E | 1.015 | 0.92 |
| 38_D | 46_F | 1.000 | 0.91 |
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 | |
| 2fs1A | 1 | 1 | 97.6 | 0.202 | Contact Map |
| 2jwsA | 1 | 1 | 97.5 | 0.218 | Contact Map |
| 2j5yA | 2 | 0.9643 | 96.6 | 0.318 | Contact Map |
| 1gjsA | 1 | 0.9643 | 96.4 | 0.327 | Contact Map |
| 1pgxA | 1 | 1 | 24 | 0.696 | Contact Map |
| 1pn5A | 1 | 0 | 21.4 | 0.703 | Contact Map |
| 2rpvA | 1 | 1 | 17 | 0.716 | Contact Map |
| 1igdA | 1 | 1 | 16.9 | 0.717 | Contact Map |
| 2khuA | 1 | 0 | 13.9 | 0.727 | Contact Map |
| 3ui3A | 2 | 0.8214 | 11 | 0.739 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)