| toxd |
| ID: | 1468427088 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 59 (57) | ||
| Sequences: | 4238 (3241.2) | ||
| Seq/Len: | 74.351 | ||
| Nf(neff/√len): | 429.3 |
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: 74.351).
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 |
| 16_C | 40_C | 4.054 | 1.00 |
| 11_R | 24_Y | 3.399 | 1.00 |
| 50_I | 54_R | 3.104 | 1.00 |
| 22_A | 46_R | 2.675 | 1.00 |
| 19_K | 36_D | 2.512 | 1.00 |
| 26_N | 33_E | 2.497 | 1.00 |
| 29_K | 33_E | 2.404 | 1.00 |
| 23_F | 50_I | 2.127 | 1.00 |
| 6_L | 56_T | 1.985 | 1.00 |
| 22_A | 48_K | 1.947 | 1.00 |
| 53_C | 57_C | 1.891 | 1.00 |
| 21_P | 34_R | 1.810 | 1.00 |
| 49_T | 52_E | 1.706 | 1.00 |
| 15_R | 41_G | 1.673 | 1.00 |
| 21_P | 36_D | 1.626 | 1.00 |
| 8_I | 27_Q | 1.618 | 1.00 |
| 54_R | 58_I | 1.543 | 1.00 |
| 9_L | 44_S | 1.412 | 1.00 |
| 24_Y | 33_E | 1.291 | 0.99 |
| 48_K | 52_E | 1.237 | 0.98 |
| 9_L | 47_F | 1.224 | 0.98 |
| 51_E | 55_R | 1.104 | 0.96 |
| 30_K | 58_I | 1.073 | 0.95 |
| 6_L | 47_F | 1.045 | 0.94 |
| 6_L | 44_S | 1.014 | 0.93 |
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 | |
| 2ddiA | 1 | 1 | 99.2 | -0.136 | Contact Map |
| 1yc0I | 1 | 1 | 99.2 | -0.125 | Contact Map |
| 1co7I | 1 | 0.6949 | 99.2 | -0.12 | Contact Map |
| 4dtgK | 1 | 0.9831 | 99.2 | -0.12 | Contact Map |
| 4bqdA | 2 | 1 | 99.2 | -0.119 | Contact Map |
| 3m7qB | 1 | 1 | 99.2 | -0.109 | Contact Map |
| 1y62A | 6 | 0.9492 | 99.2 | -0.107 | Contact Map |
| 1dtxA | 1 | 0.9831 | 99.2 | -0.105 | Contact Map |
| 1adzA | 1 | 1 | 99.2 | -0.105 | Contact Map |
| 1jc6A | 1 | 1 | 99.2 | -0.104 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)