| 1QUW |
| ID: | 1449143828 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (102) | ||
| Sequences: | 27204 (18430.1) | ||
| Seq/Len: | 266.706 | ||
| Nf(neff/√len): | 1824.9 |
HHblits Results: (2015_06)
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: 266.706).
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 |
| 83_P | 86_Q | 2.241 | 1.00 |
| 85_K | 99_Q | 2.158 | 1.00 |
| 20_V | 51_T | 2.107 | 1.00 |
| 41_E | 93_K | 2.102 | 1.00 |
| 57_V | 64_T | 2.032 | 1.00 |
| 45_A | 97_E | 2.031 | 1.00 |
| 97_E | 101_A | 2.024 | 1.00 |
| 18_K | 51_T | 1.944 | 1.00 |
| 29_C | 32_C | 1.893 | 1.00 |
| 19_P | 79_K | 1.842 | 1.00 |
| 36_A | 54_K | 1.841 | 1.00 |
| 76_I | 86_Q | 1.839 | 1.00 |
| 25_W | 54_K | 1.812 | 1.00 |
| 11_Q | 66_Q | 1.745 | 1.00 |
| 57_V | 72_I | 1.714 | 1.00 |
| 76_I | 83_P | 1.690 | 1.00 |
| 99_Q | 103_V | 1.662 | 1.00 |
| 92_P | 95_Q | 1.548 | 1.00 |
| 7_D | 62_E | 1.547 | 1.00 |
| 21_L | 75_L | 1.544 | 1.00 |
| 67_F | 78_F | 1.543 | 1.00 |
| 35_M | 75_L | 1.525 | 1.00 |
| 46_H | 97_E | 1.473 | 1.00 |
| 20_V | 53_A | 1.471 | 1.00 |
| 93_K | 97_E | 1.455 | 1.00 |
| 23_D | 75_L | 1.440 | 1.00 |
| 46_H | 101_A | 1.407 | 0.99 |
| 38_V | 93_K | 1.379 | 0.99 |
| 34_M | 90_Y | 1.351 | 0.99 |
| 6_T | 9_N | 1.345 | 0.99 |
| 38_V | 41_E | 1.344 | 0.99 |
| 78_F | 83_P | 1.344 | 0.99 |
| 23_D | 54_K | 1.341 | 0.99 |
| 9_N | 13_A | 1.336 | 0.99 |
| 87_L | 91_Q | 1.306 | 0.99 |
| 19_P | 77_L | 1.292 | 0.99 |
| 5_L | 53_A | 1.291 | 0.99 |
| 7_D | 63_T | 1.288 | 0.99 |
| 45_A | 93_K | 1.278 | 0.99 |
| 24_F | 67_F | 1.256 | 0.99 |
| 99_Q | 102_D | 1.254 | 0.99 |
| 7_D | 60_N | 1.246 | 0.98 |
| 27_A | 56_N | 1.205 | 0.98 |
| 23_D | 36_A | 1.187 | 0.98 |
| 22_V | 78_F | 1.162 | 0.97 |
| 91_Q | 95_Q | 1.156 | 0.97 |
| 77_L | 103_V | 1.138 | 0.97 |
| 56_N | 59_E | 1.119 | 0.96 |
| 77_L | 99_Q | 1.089 | 0.96 |
| 69_I | 74_T | 1.088 | 0.96 |
| 42_F | 97_E | 1.081 | 0.95 |
| 87_L | 99_Q | 1.078 | 0.95 |
| 24_F | 69_I | 1.075 | 0.95 |
| 26_A | 72_I | 1.075 | 0.95 |
| 85_K | 103_V | 1.070 | 0.95 |
| 40_E | 44_E | 1.069 | 0.95 |
| 74_T | 86_Q | 1.040 | 0.94 |
| 95_Q | 98_A | 1.012 | 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 | |
| 3f8uA | 2 | 1 | 99.8 | -0.01 | Contact Map |
| 2r2jA | 1 | 0.981 | 99.8 | 0.003 | Contact Map |
| 3apoA | 1 | 0.9238 | 99.8 | 0.007 | Contact Map |
| 2b5eA | 1 | 1 | 99.8 | 0.009 | Contact Map |
| 4ekzA | 1 | 1 | 99.7 | 0.041 | Contact Map |
| 4kcaA | 2 | 0.9905 | 99.7 | 0.052 | Contact Map |
| 4xhmA | 2 | 0 | 99.7 | 0.06 | Contact Map |
| 3ed3A | 2 | 1 | 99.7 | 0.061 | Contact Map |
| 2qgvA | 10 | 1 | 99.7 | 0.063 | Contact Map |
| 3apqA | 2 | 1 | 99.7 | 0.064 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)