| Adhiron2 |
| ID: | 1515340367 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 79 (79) | ||
| Sequences: | 1820 (1328.4) | ||
| Seq/Len: | 23.038 | ||
| Nf(neff/√len): | 149.5 |
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: 23.038).
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 |
| 29_R | 48_E | 3.312 | 1.00 |
| 34_K | 44_Y | 2.201 | 1.00 |
| 42_M | 61_K | 2.066 | 1.00 |
| 16_E | 19_K | 2.045 | 1.00 |
| 58_Y | 78_P | 2.041 | 1.00 |
| 35_E | 41_T | 2.015 | 1.00 |
| 47_L | 60_A | 1.997 | 1.00 |
| 42_M | 63_W | 1.921 | 1.00 |
| 10_A | 27_F | 1.834 | 1.00 |
| 65_K | 70_F | 1.822 | 1.00 |
| 32_K | 46_T | 1.793 | 1.00 |
| 10_A | 45_L | 1.757 | 1.00 |
| 65_K | 68_E | 1.720 | 1.00 |
| 36_Q | 42_M | 1.652 | 1.00 |
| 17_H | 60_A | 1.627 | 1.00 |
| 33_A | 45_L | 1.615 | 1.00 |
| 6_I | 33_A | 1.498 | 1.00 |
| 5_E | 64_V | 1.458 | 1.00 |
| 63_W | 70_F | 1.444 | 1.00 |
| 28_V | 50_K | 1.432 | 1.00 |
| 42_M | 74_Q | 1.391 | 0.99 |
| 17_H | 21_E | 1.375 | 0.99 |
| 25_L | 49_A | 1.365 | 0.99 |
| 31_V | 57_L | 1.358 | 0.99 |
| 16_E | 73_L | 1.345 | 0.99 |
| 49_A | 58_Y | 1.316 | 0.99 |
| 38_V | 42_M | 1.294 | 0.99 |
| 64_V | 71_K | 1.288 | 0.99 |
| 27_F | 47_L | 1.262 | 0.99 |
| 31_V | 48_E | 1.224 | 0.98 |
| 46_T | 59_E | 1.209 | 0.98 |
| 25_L | 58_Y | 1.176 | 0.98 |
| 45_L | 62_V | 1.172 | 0.98 |
| 9_L | 62_V | 1.157 | 0.97 |
| 14_V | 18_N | 1.151 | 0.97 |
| 9_L | 64_V | 1.116 | 0.96 |
| 10_A | 14_V | 1.110 | 0.96 |
| 44_Y | 59_E | 1.102 | 0.96 |
| 45_L | 60_A | 1.088 | 0.96 |
| 12_F | 73_L | 1.087 | 0.96 |
| 13_A | 60_A | 1.081 | 0.95 |
| 37_V | 41_T | 1.038 | 0.94 |
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 | |
| 2l4vA | 1 | 1 | 99.7 | -0.056 | Contact Map |
| 3ul5A | 4 | 1 | 99.6 | -0.045 | Contact Map |
| 1eqkA | 1 | 1 | 99.6 | -0.029 | Contact Map |
| 3imaB | 2 | 0.9747 | 99.6 | -0.014 | Contact Map |
| 4lziA | 1 | 1 | 99.6 | -0.007 | Contact Map |
| 4n6tA | 1 | 1 | 99.6 | -0.005 | Contact Map |
| 5a0oB | 2 | 0 | 99.6 | 0.015 | Contact Map |
| 2kxgA | 1 | 0.9747 | 99.5 | 0.048 | Contact Map |
| 3gaxA | 2 | 1 | 99.5 | 0.063 | Contact Map |
| 4n6oB | 1 | 1 | 99.5 | 0.071 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)