| gas |
| ID: | 1496149245 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 81 (80) | ||
| Sequences: | 185 (121.6) | ||
| Seq/Len: | 2.312 | ||
| Nf(neff/√len): | 13.6 |
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: 2.312).
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 |
| 64_V | 67_Y | 2.599 | 1.00 |
| 1_F | 12_L | 1.754 | 0.98 |
| 13_Y | 18_A | 1.693 | 0.97 |
| 13_Y | 73_R | 1.687 | 0.97 |
| 37_F | 53_N | 1.570 | 0.95 |
| 6_R | 14_V | 1.557 | 0.95 |
| 10_K | 39_L | 1.470 | 0.92 |
| 2_L | 79_L | 1.401 | 0.89 |
| 3_N | 70_R | 1.371 | 0.88 |
| 32_N | 62_G | 1.306 | 0.84 |
| 49_G | 54_N | 1.296 | 0.84 |
| 59_I | 65_L | 1.269 | 0.82 |
| 52_N | 59_I | 1.254 | 0.81 |
| 26_T | 67_Y | 1.246 | 0.80 |
| 74_V | 77_F | 1.229 | 0.79 |
| 15_V | 27_V | 1.229 | 0.79 |
| 29_Q | 32_N | 1.226 | 0.79 |
| 22_K | 63_C | 1.224 | 0.79 |
| 42_L | 74_V | 1.212 | 0.78 |
| 8_H | 18_A | 1.205 | 0.77 |
| 60_P | 63_C | 1.199 | 0.77 |
| 21_A | 69_V | 1.172 | 0.74 |
| 4_E | 43_A | 1.141 | 0.72 |
| 27_V | 59_I | 1.130 | 0.71 |
| 15_V | 47_L | 1.127 | 0.70 |
| 13_Y | 16_M | 1.117 | 0.69 |
| 34_N | 49_G | 1.113 | 0.69 |
| 13_Y | 27_V | 1.094 | 0.67 |
| 13_Y | 20_E | 1.090 | 0.67 |
| 33_A | 45_L | 1.080 | 0.65 |
| 17_E | 64_V | 1.080 | 0.65 |
| 22_K | 79_L | 1.070 | 0.64 |
| 21_A | 61_K | 1.069 | 0.64 |
| 3_N | 11_N | 1.066 | 0.64 |
| 20_E | 68_R | 1.064 | 0.64 |
| 33_A | 41_S | 1.047 | 0.62 |
| 78_N | 81_D | 1.042 | 0.61 |
| 1_F | 68_R | 1.035 | 0.61 |
| 4_E | 29_Q | 1.032 | 0.60 |
| 3_N | 32_N | 1.023 | 0.59 |
| 12_L | 15_V | 1.022 | 0.59 |
| 12_L | 57_V | 1.016 | 0.58 |
| 57_V | 64_V | 1.009 | 0.58 |
| 40_P | 49_G | 1.005 | 0.57 |
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 | |
| 4qt3A | 1 | 0 | 8.3 | 0.897 | Contact Map |
| 1uedA | 2 | 0.7778 | 7.7 | 0.899 | Contact Map |
| 3pm0A | 1 | 0.8025 | 7.6 | 0.899 | Contact Map |
| 1io7A | 2 | 0.7901 | 7.5 | 0.899 | Contact Map |
| 3b4xA | 1 | 0.7778 | 7.1 | 0.901 | Contact Map |
| 4qe0A | 2 | 0.8395 | 6.5 | 0.902 | Contact Map |
| 1kt0A | 1 | 0.8395 | 6.1 | 0.903 | Contact Map |
| 2jjnA | 1 | 0.7901 | 5.9 | 0.904 | Contact Map |
| 4y8wA | 3 | 0.8025 | 5.9 | 0.904 | Contact Map |
| 3b7xA | 1 | 0.7778 | 5.9 | 0.904 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)