| 1esw Amylomaltase from Thermus aquaticus 191-299 |
| ID: | 1510622751 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (109) | ||
| Sequences: | 2107 (1298.9) | ||
| Seq/Len: | 19.330 | ||
| Nf(neff/√len): | 124.4 |
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: 19.330).
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 |
| 10_K | 14_E | 2.865 | 1.00 |
| 41_W | 78_L | 2.848 | 1.00 |
| 11_A | 15_A | 2.252 | 1.00 |
| 3_F | 92_K | 2.218 | 1.00 |
| 35_V | 44_L | 2.047 | 1.00 |
| 92_K | 95_E | 2.042 | 1.00 |
| 84_S | 88_R | 2.014 | 1.00 |
| 78_L | 81_E | 1.995 | 1.00 |
| 77_V | 80_R | 1.939 | 1.00 |
| 3_F | 96_L | 1.898 | 1.00 |
| 12_E | 16_L | 1.876 | 1.00 |
| 77_V | 81_E | 1.861 | 1.00 |
| 43_H | 72_L | 1.858 | 1.00 |
| 13_A | 16_L | 1.813 | 1.00 |
| 79_E | 83_F | 1.808 | 1.00 |
| 88_R | 91_E | 1.790 | 1.00 |
| 41_W | 81_E | 1.788 | 1.00 |
| 27_F | 72_L | 1.771 | 1.00 |
| 1_L | 4_R | 1.764 | 1.00 |
| 35_V | 42_F | 1.764 | 1.00 |
| 43_H | 74_R | 1.733 | 1.00 |
| 81_E | 84_S | 1.716 | 1.00 |
| 14_E | 98_H | 1.707 | 1.00 |
| 74_R | 77_V | 1.688 | 1.00 |
| 21_I | 99_L | 1.664 | 1.00 |
| 93_A | 97_F | 1.654 | 1.00 |
| 93_A | 100_V | 1.651 | 1.00 |
| 54_A | 70_N | 1.635 | 1.00 |
| 40_E | 77_V | 1.603 | 1.00 |
| 39_P | 48_G | 1.461 | 1.00 |
| 26_I | 107_G | 1.407 | 0.99 |
| 43_H | 52_V | 1.369 | 0.99 |
| 7_G | 11_A | 1.339 | 0.99 |
| 81_E | 85_F | 1.331 | 0.99 |
| 94_L | 100_V | 1.253 | 0.99 |
| 56_V | 60_Y | 1.238 | 0.98 |
| 24_M | 93_A | 1.221 | 0.98 |
| 10_K | 98_H | 1.168 | 0.97 |
| 40_E | 81_E | 1.160 | 0.97 |
| 58_P | 65_G | 1.155 | 0.97 |
| 87_I | 91_E | 1.129 | 0.97 |
| 106_R | 109_E | 1.114 | 0.96 |
| 39_P | 49_R | 1.102 | 0.96 |
| 28_V | 34_E | 1.098 | 0.96 |
| 92_K | 96_L | 1.064 | 0.95 |
| 86_W | 90_L | 1.026 | 0.94 |
| 82_G | 87_I | 1.014 | 0.93 |
| 46_E | 49_R | 1.010 | 0.93 |
| 60_Y | 63_E | 1.001 | 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 | |
| 1eswA | 1 | 1 | 100 | -0.07 | Contact Map |
| 1tz7A | 2 | 1 | 100 | -0.069 | Contact Map |
| 1x1nA | 1 | 1 | 100 | -0.069 | Contact Map |
| 4s3qA | 3 | 0 | 100 | -0.036 | Contact Map |
| 4u33A | 6 | 0 | 94.2 | 0.854 | Contact Map |
| 4hphA | 1 | 0.9174 | 92.8 | 0.861 | Contact Map |
| 3k1dA | 1 | 0.8899 | 92.7 | 0.862 | Contact Map |
| 4jcmA | 1 | 0.9083 | 91.9 | 0.865 | Contact Map |
| 1zjaA | 2 | 0.9174 | 91.8 | 0.866 | Contact Map |
| 3amlA | 1 | 0.8807 | 91.5 | 0.867 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)