| 1EKGA |
| ID: | 1411763047 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (111) | ||
| Sequences: | 473 (339.3) | ||
| Seq/Len: | 4.261 | ||
| Nf(neff/√len): | 32.2 |
HHblits Results: (2013_03)
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: 4.261).
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 |
| 64_Q | 78_D | 2.938 | 1.00 |
| 3_E | 63_K | 2.523 | 1.00 |
| 2_D | 5_T | 2.247 | 1.00 |
| 9_L | 79_W | 1.922 | 1.00 |
| 6_Y | 60_T | 1.908 | 1.00 |
| 77_Y | 89_D | 1.792 | 1.00 |
| 91_V | 99_A | 1.756 | 0.99 |
| 52_G | 74_P | 1.731 | 0.99 |
| 92_S | 95_E | 1.726 | 0.99 |
| 69_S | 100_E | 1.645 | 0.99 |
| 77_Y | 91_V | 1.631 | 0.99 |
| 7_E | 11_E | 1.615 | 0.99 |
| 59_Q | 62_N | 1.580 | 0.99 |
| 3_E | 60_T | 1.562 | 0.98 |
| 41_G | 64_Q | 1.469 | 0.97 |
| 7_E | 58_K | 1.460 | 0.97 |
| 68_S | 74_P | 1.453 | 0.97 |
| 99_A | 103_K | 1.451 | 0.97 |
| 43_L | 47_L | 1.432 | 0.97 |
| 64_Q | 87_S | 1.410 | 0.97 |
| 20_F | 111_L | 1.397 | 0.96 |
| 53_T | 74_P | 1.395 | 0.96 |
| 10_A | 14_L | 1.381 | 0.96 |
| 44_T | 53_T | 1.371 | 0.96 |
| 69_S | 72_S | 1.351 | 0.95 |
| 72_S | 100_E | 1.332 | 0.95 |
| 36_V | 43_L | 1.326 | 0.95 |
| 25_A | 34_Y | 1.295 | 0.94 |
| 56_I | 96_L | 1.286 | 0.93 |
| 12_E | 35_D | 1.258 | 0.92 |
| 86_Y | 89_D | 1.257 | 0.92 |
| 78_D | 87_S | 1.254 | 0.92 |
| 69_S | 104_A | 1.217 | 0.91 |
| 18_A | 26_D | 1.201 | 0.90 |
| 75_K | 86_Y | 1.194 | 0.90 |
| 43_L | 88_H | 1.192 | 0.89 |
| 48_G | 52_G | 1.186 | 0.89 |
| 38_F | 86_Y | 1.166 | 0.88 |
| 62_N | 76_R | 1.156 | 0.87 |
| 83_N | 92_S | 1.151 | 0.87 |
| 67_L | 93_L | 1.150 | 0.87 |
| 13_T | 94_H | 1.132 | 0.86 |
| 2_D | 39_G | 1.125 | 0.86 |
| 37_S | 77_Y | 1.110 | 0.84 |
| 79_W | 85_V | 1.092 | 0.83 |
| 36_V | 45_V | 1.071 | 0.81 |
| 67_L | 86_Y | 1.059 | 0.80 |
| 13_T | 65_I | 1.039 | 0.79 |
| 6_Y | 63_K | 1.035 | 0.78 |
| 42_V | 60_T | 1.033 | 0.78 |
| 52_G | 72_S | 1.031 | 0.78 |
| 57_N | 62_N | 1.020 | 0.77 |
| 41_G | 62_N | 1.020 | 0.77 |
| 54_Y | 70_P | 1.015 | 0.76 |
| 15_D | 95_E | 1.014 | 0.76 |
| 13_T | 75_K | 1.007 | 0.76 |
| 6_Y | 48_G | 1.005 | 0.75 |
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 | |
| 3t3lA | 1 | 1 | 100 | 0.021 | Contact Map |
| 1ew4A | 1 | 0.8908 | 100 | 0.108 | Contact Map |
| 3oeqA | 1 | 0.8655 | 100 | 0.123 | Contact Map |
| 4jpdA | 1 | 0.9076 | 100 | 0.126 | Contact Map |
| 4hs5A | 2 | 0.8824 | 100 | 0.137 | Contact Map |
| 4gwpD | 1 | 0.8151 | 15.7 | 0.929 | Contact Map |
| 3phfA | 16 | 0.6723 | 10.5 | 0.934 | Contact Map |
| 3gr5A | 1 | 0.3529 | 8.6 | 0.936 | Contact Map |
| 2pnyA | 1 | 0.8992 | 8.4 | 0.937 | Contact Map |
| 1qf6A | 1 | 0.8571 | 7.4 | 0.938 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)