| Martyna |
| ID: | 1512656563 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 95 (89) | ||
| Sequences: | 268 (162.9) | ||
| Seq/Len: | 3.011 | ||
| Nf(neff/√len): | 17.3 |
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: 3.011).
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 |
| 30_T | 60_T | 2.967 | 1.00 |
| 14_L | 45_S | 2.345 | 1.00 |
| 61_R | 65_H | 2.209 | 1.00 |
| 61_R | 80_D | 2.042 | 1.00 |
| 44_K | 47_C | 1.951 | 1.00 |
| 27_L | 51_Y | 1.912 | 0.99 |
| 65_H | 80_D | 1.835 | 0.99 |
| 19_T | 22_Q | 1.676 | 0.98 |
| 8_I | 50_T | 1.612 | 0.97 |
| 14_L | 40_I | 1.565 | 0.97 |
| 23_L | 40_I | 1.563 | 0.97 |
| 39_W | 44_K | 1.507 | 0.96 |
| 58_V | 81_Y | 1.478 | 0.95 |
| 12_S | 23_L | 1.468 | 0.95 |
| 10_H | 46_H | 1.448 | 0.94 |
| 3_G | 6_S | 1.422 | 0.94 |
| 53_T | 56_E | 1.408 | 0.93 |
| 43_I | 50_T | 1.405 | 0.93 |
| 15_V | 75_K | 1.387 | 0.93 |
| 87_L | 90_H | 1.367 | 0.92 |
| 27_L | 75_K | 1.353 | 0.91 |
| 14_L | 23_L | 1.326 | 0.90 |
| 24_K | 38_F | 1.269 | 0.88 |
| 41_D | 75_K | 1.240 | 0.86 |
| 33_L | 50_T | 1.185 | 0.82 |
| 3_G | 90_H | 1.117 | 0.77 |
| 38_F | 47_C | 1.116 | 0.77 |
| 15_V | 66_G | 1.113 | 0.76 |
| 61_R | 81_Y | 1.107 | 0.76 |
| 69_W | 73_N | 1.106 | 0.76 |
| 39_W | 55_E | 1.106 | 0.76 |
| 69_W | 81_Y | 1.098 | 0.75 |
| 50_T | 86_E | 1.094 | 0.75 |
| 13_N | 21_G | 1.080 | 0.73 |
| 19_T | 44_K | 1.079 | 0.73 |
| 34_V | 39_W | 1.028 | 0.68 |
| 18_F | 69_W | 1.027 | 0.68 |
| 64_L | 69_W | 1.024 | 0.67 |
| 87_L | 91_R | 1.022 | 0.67 |
| 39_W | 48_F | 1.021 | 0.67 |
| 23_L | 42_K | 1.003 | 0.65 |
| 27_L | 49_V | 1.000 | 0.65 |
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 | |
| 3pgwS | 2 | 0.8737 | 98.8 | 0.699 | Contact Map |
| 4fxwA | 2 | 0.9368 | 98.8 | 0.708 | Contact Map |
| 3ue2A | 1 | 0.9579 | 98.7 | 0.715 | Contact Map |
| 2wbrA | 1 | 0.9263 | 98.7 | 0.718 | Contact Map |
| 3s6eA | 2 | 0.9684 | 98.6 | 0.72 | Contact Map |
| 2cq2A | 1 | 0.9474 | 98.6 | 0.72 | Contact Map |
| 2pe8A | 1 | 0.9684 | 98.6 | 0.722 | Contact Map |
| 3r27A | 2 | 0.8842 | 98.6 | 0.723 | Contact Map |
| 2dnhA | 1 | 0.9789 | 98.6 | 0.725 | Contact Map |
| 3s8sA | 1 | 0.9579 | 98.6 | 0.725 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)