| 1BE9 |
| ID: | 1488386423 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 115 (101) | ||
| Sequences: | 1574 (864.2) | ||
| Seq/Len: | 15.584 | ||
| Nf(neff/√len): | 86.0 |
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: 15.584).
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 |
| 53_L | 90_A | 4.711 | 1.00 |
| 61_S | 89_I | 2.542 | 1.00 |
| 72_H | 76_A | 2.463 | 1.00 |
| 44_G | 48_D | 2.419 | 1.00 |
| 67_L | 70_A | 2.150 | 1.00 |
| 70_A | 75_A | 1.938 | 1.00 |
| 36_I | 75_A | 1.894 | 1.00 |
| 38_I | 53_L | 1.787 | 1.00 |
| 12_R | 92_Y | 1.732 | 1.00 |
| 61_S | 64_G | 1.694 | 1.00 |
| 43_A | 48_D | 1.659 | 1.00 |
| 28_I | 39_S | 1.598 | 1.00 |
| 35_G | 58_Q | 1.592 | 1.00 |
| 46_P | 50_S | 1.486 | 1.00 |
| 75_A | 78_A | 1.478 | 1.00 |
| 74_Q | 77_I | 1.450 | 1.00 |
| 29_G | 72_H | 1.418 | 1.00 |
| 23_L | 79_L | 1.364 | 0.99 |
| 15_V | 87_T | 1.362 | 0.99 |
| 26_N | 39_S | 1.311 | 0.99 |
| 102_A | 106_V | 1.287 | 0.99 |
| 79_L | 88_I | 1.282 | 0.99 |
| 27_I | 72_H | 1.265 | 0.99 |
| 67_L | 75_A | 1.261 | 0.99 |
| 21_T | 49_L | 1.237 | 0.98 |
| 29_G | 59_I | 1.221 | 0.98 |
| 73_E | 77_I | 1.218 | 0.98 |
| 93_K | 96_E | 1.216 | 0.98 |
| 30_G | 75_A | 1.203 | 0.98 |
| 13_R | 87_T | 1.202 | 0.98 |
| 66_D | 70_A | 1.194 | 0.98 |
| 69_N | 91_Q | 1.188 | 0.98 |
| 26_N | 40_F | 1.160 | 0.97 |
| 41_I | 50_S | 1.141 | 0.97 |
| 56_G | 60_L | 1.132 | 0.97 |
| 17_H | 84_Q | 1.116 | 0.96 |
| 82_A | 86_V | 1.097 | 0.96 |
| 70_A | 78_A | 1.094 | 0.96 |
| 13_R | 89_I | 1.091 | 0.96 |
| 70_A | 74_Q | 1.090 | 0.96 |
| 101_E | 104_S | 1.089 | 0.96 |
| 22_G | 46_P | 1.081 | 0.95 |
| 58_Q | 93_K | 1.059 | 0.95 |
| 26_N | 72_H | 1.058 | 0.95 |
| 26_N | 42_L | 1.053 | 0.95 |
| 12_R | 52_E | 1.042 | 0.94 |
| 30_G | 72_H | 1.031 | 0.94 |
| 94_P | 98_S | 1.008 | 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 | |
| 2xkxA | 2 | 1 | 99.7 | 0.379 | Contact Map |
| 1tp5A | 1 | 1 | 99.7 | 0.379 | Contact Map |
| 1um7A | 1 | 0.9391 | 99.5 | 0.432 | Contact Map |
| 3i4wA | 4 | 0.8435 | 99.5 | 0.434 | Contact Map |
| 2dazA | 1 | 0.9304 | 99.5 | 0.452 | Contact Map |
| 3ggeA | 3 | 0.8087 | 99.5 | 0.452 | Contact Map |
| 2eeiA | 1 | 0.9217 | 99.5 | 0.455 | Contact Map |
| 2iwoA | 2 | 0.8783 | 99.4 | 0.461 | Contact Map |
| 1z87A | 1 | 1 | 99.4 | 0.462 | Contact Map |
| 1uhpA | 1 | 0.8522 | 99.4 | 0.462 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)