| 1esw Amylomaltase from Thermus aquaticus 321-500 |
| ID: | 1510622987 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 180 (166) | ||
| Sequences: | 2373 (1493.1) | ||
| Seq/Len: | 14.295 | ||
| Nf(neff/√len): | 115.9 |
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: 14.295).
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 |
| 77_D | 139_S | 3.746 | 1.00 |
| 134_V | 170_L | 3.634 | 1.00 |
| 69_V | 119_G | 3.592 | 1.00 |
| 71_T | 130_P | 3.292 | 1.00 |
| 67_V | 124_A | 3.278 | 1.00 |
| 113_W | 169_R | 2.625 | 1.00 |
| 120_M | 129_Y | 2.485 | 1.00 |
| 96_R | 172_A | 2.472 | 1.00 |
| 112_P | 136_A | 2.471 | 1.00 |
| 78_T | 81_G | 2.378 | 1.00 |
| 121_K | 177_T | 2.324 | 1.00 |
| 31_A | 35_R | 2.251 | 1.00 |
| 120_M | 174_A | 2.065 | 1.00 |
| 61_Y | 69_V | 2.012 | 1.00 |
| 72_G | 76_N | 1.968 | 1.00 |
| 45_Q | 79_T | 1.857 | 1.00 |
| 41_M | 70_Y | 1.831 | 1.00 |
| 171_R | 180_L | 1.810 | 1.00 |
| 151_G | 154_A | 1.797 | 1.00 |
| 131_V | 157_L | 1.794 | 1.00 |
| 119_G | 127_A | 1.792 | 1.00 |
| 47_A | 56_F | 1.790 | 1.00 |
| 42_K | 67_V | 1.765 | 1.00 |
| 148_R | 152_N | 1.687 | 1.00 |
| 171_R | 175_E | 1.675 | 1.00 |
| 80_L | 84_R | 1.646 | 1.00 |
| 83_Y | 111_V | 1.624 | 1.00 |
| 64_H | 125_R | 1.593 | 1.00 |
| 59_H | 97_Y | 1.583 | 1.00 |
| 172_A | 176_A | 1.559 | 1.00 |
| 69_V | 124_A | 1.549 | 1.00 |
| 30_E | 33_R | 1.538 | 1.00 |
| 46_F | 76_N | 1.533 | 1.00 |
| 30_E | 34_D | 1.522 | 1.00 |
| 117_H | 176_A | 1.517 | 1.00 |
| 116_M | 129_Y | 1.513 | 1.00 |
| 25_I | 30_E | 1.487 | 1.00 |
| 21_D | 30_E | 1.451 | 1.00 |
| 98_L | 118_L | 1.433 | 1.00 |
| 80_L | 112_P | 1.405 | 0.99 |
| 80_L | 136_A | 1.385 | 0.99 |
| 77_D | 85_T | 1.364 | 0.99 |
| 63_A | 125_R | 1.350 | 0.99 |
| 170_L | 174_A | 1.349 | 0.99 |
| 27_P | 31_A | 1.342 | 0.99 |
| 120_M | 127_A | 1.336 | 0.99 |
| 77_D | 81_G | 1.326 | 0.99 |
| 172_A | 175_E | 1.299 | 0.99 |
| 42_K | 56_F | 1.295 | 0.99 |
| 83_Y | 95_A | 1.287 | 0.99 |
| 93_F | 96_R | 1.278 | 0.99 |
| 81_G | 139_S | 1.276 | 0.99 |
| 9_Q | 12_F | 1.275 | 0.99 |
| 84_R | 138_G | 1.242 | 0.98 |
| 79_T | 130_P | 1.229 | 0.98 |
| 110_E | 114_A | 1.227 | 0.98 |
| 42_K | 62_P | 1.211 | 0.98 |
| 87_T | 91_K | 1.199 | 0.98 |
| 175_E | 180_L | 1.156 | 0.97 |
| 168_A | 172_A | 1.148 | 0.97 |
| 79_T | 115_L | 1.138 | 0.97 |
| 50_D | 53_E | 1.126 | 0.97 |
| 118_L | 122_S | 1.118 | 0.96 |
| 132_Q | 143_M | 1.100 | 0.96 |
| 28_E | 31_A | 1.083 | 0.96 |
| 24_V | 30_E | 1.076 | 0.95 |
| 68_V | 128_V | 1.061 | 0.95 |
| 120_M | 134_V | 1.059 | 0.95 |
| 117_H | 177_T | 1.048 | 0.94 |
| 21_D | 42_K | 1.040 | 0.94 |
| 21_D | 29_V | 1.039 | 0.94 |
| 10_E | 14_E | 1.028 | 0.94 |
| 43_V | 70_Y | 1.018 | 0.93 |
| 17_V | 38_L | 1.017 | 0.93 |
| 19_A | 33_R | 1.013 | 0.93 |
| 10_E | 13_G | 1.012 | 0.93 |
| 169_R | 172_A | 1.008 | 0.93 |
| 27_P | 30_E | 1.002 | 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 | 0.9889 | 100 | 0.059 | Contact Map |
| 1x1nA | 1 | 0.9611 | 100 | 0.073 | Contact Map |
| 1tz7A | 2 | 0.95 | 100 | 0.083 | Contact Map |
| 4s3qA | 3 | 0 | 100 | 0.124 | Contact Map |
| 4bzyA | 3 | 0.9444 | 71.2 | 0.918 | Contact Map |
| 2wanA | 1 | 0.8778 | 67.3 | 0.921 | Contact Map |
| 4e2oA | 1 | 0.8111 | 63.5 | 0.923 | Contact Map |
| 4j7rA | 2 | 0.9611 | 61.5 | 0.924 | Contact Map |
| 3amlA | 1 | 0.95 | 58 | 0.925 | Contact Map |
| 1ji1A | 2 | 0.8222 | 56.8 | 0.926 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)