| flexbb_double_size |
| ID: | 1496585664 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 965 (603.3) | ||
| Seq/Len: | 11.092 | ||
| Nf(neff/√len): | 64.7 |
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: 11.092).
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 |
| 14_L | 81_L | 2.143 | 1.00 |
| 22_L | 61_Y | 2.116 | 1.00 |
| 13_A | 22_L | 1.749 | 1.00 |
| 25_S | 76_T | 1.633 | 1.00 |
| 4_Y | 78_I | 1.573 | 1.00 |
| 4_Y | 82_H | 1.555 | 1.00 |
| 22_L | 81_L | 1.542 | 1.00 |
| 12_P | 16_D | 1.532 | 1.00 |
| 4_Y | 54_S | 1.522 | 1.00 |
| 6_F | 87_A | 1.495 | 1.00 |
| 5_F | 62_L | 1.451 | 1.00 |
| 26_A | 77_L | 1.417 | 1.00 |
| 58_G | 70_A | 1.403 | 0.99 |
| 23_C | 29_Y | 1.383 | 0.99 |
| 1_V | 64_L | 1.374 | 0.99 |
| 13_A | 23_C | 1.330 | 0.99 |
| 5_F | 8_I | 1.324 | 0.99 |
| 9_H | 50_L | 1.323 | 0.99 |
| 53_S | 66_S | 1.315 | 0.99 |
| 14_L | 57_L | 1.308 | 0.99 |
| 15_T | 57_L | 1.260 | 0.99 |
| 25_S | 51_S | 1.254 | 0.99 |
| 55_L | 80_T | 1.209 | 0.98 |
| 37_F | 54_S | 1.206 | 0.98 |
| 8_I | 14_L | 1.203 | 0.98 |
| 13_A | 24_S | 1.197 | 0.98 |
| 50_L | 86_V | 1.189 | 0.98 |
| 23_C | 62_L | 1.166 | 0.97 |
| 23_C | 40_R | 1.151 | 0.97 |
| 42_F | 48_V | 1.141 | 0.97 |
| 22_L | 63_I | 1.131 | 0.97 |
| 38_G | 45_F | 1.066 | 0.95 |
| 56_S | 85_S | 1.044 | 0.94 |
| 1_V | 15_T | 1.041 | 0.94 |
| 48_V | 60_L | 1.039 | 0.94 |
| 24_S | 61_Y | 1.039 | 0.94 |
| 14_L | 55_L | 1.030 | 0.94 |
| 46_N | 63_I | 1.026 | 0.94 |
| 6_F | 70_A | 1.025 | 0.93 |
| 53_S | 57_L | 1.019 | 0.93 |
| 44_L | 71_N | 1.015 | 0.93 |
| 31_A | 77_L | 1.010 | 0.93 |
| 43_D | 82_H | 1.009 | 0.93 |
| 16_D | 51_S | 1.008 | 0.93 |
| 23_C | 87_A | 1.003 | 0.93 |
| 50_L | 83_A | 1.000 | 0.92 |
| 39_G | 78_I | 1.000 | 0.92 |
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 | |
| 3ccdA | 2 | 0.977 | 93.5 | 0.837 | Contact Map |
| 1ka5A | 1 | 1 | 93 | 0.84 | Contact Map |
| 1kklH | 3 | 1 | 92.9 | 0.84 | Contact Map |
| 1ptfA | 1 | 1 | 92.6 | 0.842 | Contact Map |
| 1y51A | 3 | 0.9885 | 91.7 | 0.846 | Contact Map |
| 1sphA | 2 | 0.9885 | 91.3 | 0.848 | Contact Map |
| 3ihsA | 2 | 0.9425 | 91.1 | 0.849 | Contact Map |
| 1pchA | 1 | 0.9885 | 90.4 | 0.851 | Contact Map |
| 3le1A | 2 | 0.9885 | 87.9 | 0.858 | Contact Map |
| 3ulkA | 2 | 0.8736 | 9 | 0.927 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)