| 1esw Amylomaltase from Thermus aquaticus 1-98 |
| ID: | 1510622604 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 98 (96) | ||
| Sequences: | 2228 (1235.4) | ||
| Seq/Len: | 23.208 | ||
| Nf(neff/√len): | 126.1 |
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: 23.208).
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_T | 71_L | 3.389 | 1.00 |
| 7_F | 41_G | 3.016 | 1.00 |
| 36_L | 41_G | 2.702 | 1.00 |
| 26_G | 73_D | 2.695 | 1.00 |
| 24_V | 73_D | 2.522 | 1.00 |
| 18_G | 27_R | 2.108 | 1.00 |
| 9_L | 36_L | 2.098 | 1.00 |
| 35_F | 39_A | 1.745 | 1.00 |
| 28_E | 31_D | 1.723 | 1.00 |
| 20_Y | 74_L | 1.676 | 1.00 |
| 6_A | 43_Y | 1.601 | 1.00 |
| 73_D | 76_P | 1.584 | 1.00 |
| 6_A | 42_R | 1.546 | 1.00 |
| 63_S | 66_A | 1.522 | 1.00 |
| 25_L | 67_G | 1.509 | 1.00 |
| 56_D | 60_Q | 1.484 | 1.00 |
| 12_H | 71_L | 1.478 | 1.00 |
| 52_T | 56_D | 1.361 | 0.99 |
| 61_S | 64_A | 1.325 | 0.99 |
| 53_G | 62_F | 1.304 | 0.99 |
| 24_V | 28_E | 1.300 | 0.99 |
| 10_L | 47_L | 1.298 | 0.99 |
| 32_F | 44_W | 1.286 | 0.99 |
| 50_G | 61_S | 1.263 | 0.99 |
| 76_P | 79_E | 1.224 | 0.98 |
| 30_R | 34_R | 1.222 | 0.98 |
| 13_P | 46_V | 1.217 | 0.98 |
| 53_G | 56_D | 1.216 | 0.98 |
| 13_P | 71_L | 1.206 | 0.98 |
| 50_G | 64_A | 1.205 | 0.98 |
| 27_R | 31_D | 1.194 | 0.98 |
| 30_R | 76_P | 1.178 | 0.98 |
| 20_Y | 24_V | 1.176 | 0.98 |
| 30_R | 33_L | 1.175 | 0.98 |
| 28_E | 40_G | 1.110 | 0.96 |
| 18_G | 28_E | 1.097 | 0.96 |
| 26_G | 76_P | 1.091 | 0.96 |
| 87_D | 92_Q | 1.091 | 0.96 |
| 12_H | 47_L | 1.079 | 0.95 |
| 88_P | 92_Q | 1.074 | 0.95 |
| 89_G | 92_Q | 1.068 | 0.95 |
| 52_T | 62_F | 1.052 | 0.95 |
| 10_L | 45_Q | 1.048 | 0.94 |
| 13_P | 49_L | 1.027 | 0.94 |
| 11_L | 32_F | 1.024 | 0.93 |
| 22_V | 70_Y | 1.023 | 0.93 |
| 14_T | 64_A | 1.013 | 0.93 |
| 24_V | 27_R | 1.009 | 0.93 |
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 | 0.059 | Contact Map |
| 1tz7A | 2 | 1 | 100 | 0.073 | Contact Map |
| 4s3qA | 3 | 0 | 100 | 0.075 | Contact Map |
| 1x1nA | 1 | 1 | 100 | 0.086 | Contact Map |
| 1ht6A | 1 | 0.898 | 96.3 | 0.784 | Contact Map |
| 1ud2A | 1 | 0.9388 | 95.5 | 0.798 | Contact Map |
| 3bh4A | 2 | 0.9184 | 95.3 | 0.802 | Contact Map |
| 1wpcA | 1 | 0.9184 | 95.3 | 0.802 | Contact Map |
| 2ze0A | 1 | 0.9592 | 95 | 0.804 | Contact Map |
| 2zicA | 1 | 0.949 | 95 | 0.805 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)