| fastrelax bb |
| ID: | 1505158896 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 487 (166.5) | ||
| Seq/Len: | 5.598 | ||
| Nf(neff/√len): | 17.9 |
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: 5.598).
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 |
| 22_L | 80_L | 2.092 | 1.00 |
| 14_L | 62_L | 1.892 | 1.00 |
| 42_I | 72_D | 1.811 | 1.00 |
| 4_Y | 82_E | 1.768 | 1.00 |
| 4_Y | 78_V | 1.570 | 0.99 |
| 60_D | 77_T | 1.529 | 0.99 |
| 14_L | 55_V | 1.512 | 0.99 |
| 8_V | 86_F | 1.457 | 0.99 |
| 15_R | 49_Q | 1.451 | 0.98 |
| 28_I | 81_L | 1.433 | 0.98 |
| 30_A | 55_V | 1.431 | 0.98 |
| 30_A | 64_V | 1.416 | 0.98 |
| 32_I | 71_I | 1.379 | 0.98 |
| 6_L | 62_L | 1.371 | 0.98 |
| 5_W | 23_V | 1.332 | 0.97 |
| 14_L | 74_L | 1.330 | 0.97 |
| 23_V | 52_G | 1.325 | 0.97 |
| 35_L | 42_I | 1.320 | 0.97 |
| 32_I | 51_L | 1.312 | 0.97 |
| 12_H | 41_L | 1.295 | 0.96 |
| 40_I | 51_L | 1.268 | 0.96 |
| 51_L | 81_L | 1.255 | 0.95 |
| 25_R | 76_F | 1.254 | 0.95 |
| 6_L | 54_D | 1.240 | 0.95 |
| 49_Q | 79_R | 1.237 | 0.95 |
| 49_Q | 68_E | 1.171 | 0.92 |
| 23_V | 59_S | 1.167 | 0.92 |
| 32_I | 63_L | 1.158 | 0.92 |
| 1_H | 76_F | 1.152 | 0.92 |
| 43_L | 56_D | 1.117 | 0.90 |
| 32_I | 70_A | 1.096 | 0.89 |
| 36_H | 45_L | 1.089 | 0.88 |
| 9_F | 22_L | 1.068 | 0.87 |
| 4_Y | 28_I | 1.065 | 0.87 |
| 36_H | 51_L | 1.065 | 0.87 |
| 41_L | 51_L | 1.065 | 0.87 |
| 41_L | 49_Q | 1.063 | 0.87 |
| 3_S | 57_R | 1.062 | 0.87 |
| 10_D | 18_S | 1.057 | 0.86 |
| 35_L | 64_V | 1.054 | 0.86 |
| 19_A | 72_D | 1.046 | 0.86 |
| 37_F | 85_R | 1.038 | 0.85 |
| 16_S | 63_L | 1.035 | 0.85 |
| 35_L | 79_R | 1.033 | 0.85 |
| 5_W | 8_V | 1.027 | 0.84 |
| 70_A | 75_L | 1.018 | 0.83 |
| 37_F | 59_S | 1.015 | 0.83 |
| 6_L | 52_G | 1.008 | 0.83 |
| 4_Y | 74_L | 1.004 | 0.82 |
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 | |
| 1kklH | 3 | 1 | 97.8 | 0.787 | Contact Map |
| 1ka5A | 1 | 1 | 97.8 | 0.789 | Contact Map |
| 1ptfA | 1 | 1 | 97.8 | 0.789 | Contact Map |
| 1sphA | 2 | 0.9885 | 97.7 | 0.793 | Contact Map |
| 1pchA | 1 | 0.9885 | 97.7 | 0.793 | Contact Map |
| 1y51A | 3 | 0.9885 | 97.7 | 0.794 | Contact Map |
| 3ccdA | 2 | 0.977 | 97.5 | 0.801 | Contact Map |
| 3ihsA | 2 | 0.9425 | 97.5 | 0.802 | Contact Map |
| 3le1A | 2 | 0.9885 | 97.4 | 0.807 | Contact Map |
| 1vhfA | 1 | 0.3218 | 10.4 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)