| sandwich_2 |
| ID: | 1473155224 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 69 (68) | ||
| Sequences: | 561 (429.7) | ||
| Seq/Len: | 8.250 | ||
| Nf(neff/√len): | 52.1 |
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: 8.250).
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_A | 45_W | 2.384 | 1.00 |
| 43_R | 48_E | 2.246 | 1.00 |
| 29_G | 33_D | 2.003 | 1.00 |
| 47_G | 50_L | 1.785 | 1.00 |
| 25_W | 29_G | 1.755 | 1.00 |
| 39_T | 56_T | 1.569 | 1.00 |
| 38_N | 45_W | 1.520 | 1.00 |
| 49_T | 62_S | 1.430 | 0.99 |
| 25_W | 28_I | 1.413 | 0.99 |
| 15_P | 18_T | 1.386 | 0.99 |
| 5_I | 64_F | 1.385 | 0.99 |
| 7_S | 10_D | 1.364 | 0.99 |
| 55_N | 59_P | 1.356 | 0.99 |
| 63_I | 66_D | 1.325 | 0.99 |
| 60_K | 65_K | 1.246 | 0.98 |
| 21_G | 26_D | 1.222 | 0.97 |
| 44_P | 48_E | 1.200 | 0.97 |
| 43_R | 61_M | 1.182 | 0.97 |
| 31_L | 46_A | 1.145 | 0.96 |
| 9_G | 13_A | 1.113 | 0.95 |
| 6_F | 65_K | 1.103 | 0.94 |
| 6_F | 36_K | 1.091 | 0.94 |
| 12_S | 16_A | 1.082 | 0.94 |
| 7_S | 28_I | 1.081 | 0.94 |
| 12_S | 56_T | 1.075 | 0.93 |
| 13_A | 16_A | 1.074 | 0.93 |
| 6_F | 34_R | 1.068 | 0.93 |
| 32_A | 39_T | 1.056 | 0.93 |
| 30_S | 33_D | 1.054 | 0.92 |
| 29_G | 34_R | 1.054 | 0.92 |
| 12_S | 17_S | 1.045 | 0.92 |
| 5_I | 8_D | 1.036 | 0.92 |
| 19_G | 22_G | 1.033 | 0.91 |
| 32_A | 35_K | 1.023 | 0.91 |
| 13_A | 63_I | 1.022 | 0.91 |
| 35_K | 47_G | 1.016 | 0.90 |
| 63_I | 68_T | 1.013 | 0.90 |
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 | |
| 1oxzA | 1 | 0.058 | 2.7 | 0.863 | Contact Map |
| 4xjnA | 13 | 0 | 1.6 | 0.88 | Contact Map |
| 2yd0A | 1 | 0.4058 | 1.3 | 0.886 | Contact Map |
| 1yfsA | 2 | 0.8116 | 1.3 | 0.886 | Contact Map |
| 3oqqA | 1 | 0.1884 | 1.2 | 0.889 | Contact Map |
| 1wlfA | 1 | 0.8696 | 1.1 | 0.892 | Contact Map |
| 3f1fN | 1 | 0.3043 | 1 | 0.893 | Contact Map |
| 2k8eA | 1 | 0.2319 | 1 | 0.894 | Contact Map |
| 4tp9J | 1 | 0.3333 | 1 | 0.894 | Contact Map |
| 4rb6N | 1 | 0.3333 | 1 | 0.894 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)