| TargetPilE 1-70 |
| ID: | 1513816953 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (65) | ||
| Sequences: | 11071 (8176.4) | ||
| Seq/Len: | 170.323 | ||
| Nf(neff/√len): | 1014.2 |
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: 170.323).
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 |
| 47_A | 51_Q | 2.898 | 1.00 |
| 62_A | 66_D | 2.484 | 1.00 |
| 40_K | 44_A | 2.193 | 1.00 |
| 32_A | 36_Y | 2.119 | 1.00 |
| 45_A | 48_A | 1.930 | 1.00 |
| 53_A | 57_S | 1.784 | 1.00 |
| 57_S | 61_A | 1.740 | 1.00 |
| 59_L | 63_Y | 1.731 | 1.00 |
| 48_A | 51_Q | 1.670 | 1.00 |
| 53_A | 56_M | 1.656 | 1.00 |
| 38_K | 41_R | 1.651 | 1.00 |
| 36_Y | 40_K | 1.594 | 1.00 |
| 54_S | 58_E | 1.571 | 1.00 |
| 56_M | 60_A | 1.419 | 1.00 |
| 45_A | 49_T | 1.408 | 1.00 |
| 39_Y | 42_K | 1.315 | 0.99 |
| 31_V | 34_P | 1.292 | 0.99 |
| 46_S | 49_T | 1.269 | 0.99 |
| 34_P | 37_T | 1.250 | 0.99 |
| 61_A | 65_D | 1.238 | 0.98 |
| 33_I | 37_T | 1.219 | 0.98 |
| 7_E | 11_K | 1.178 | 0.98 |
| 8_N | 11_K | 1.171 | 0.98 |
| 54_S | 57_S | 1.168 | 0.97 |
| 60_A | 63_Y | 1.116 | 0.96 |
| 51_Q | 55_C | 1.111 | 0.96 |
| 50_G | 54_S | 1.101 | 0.96 |
| 42_K | 46_S | 1.071 | 0.95 |
| 41_R | 45_A | 1.062 | 0.95 |
| 63_Y | 68_T | 1.054 | 0.95 |
| 48_A | 59_L | 1.053 | 0.95 |
| 40_K | 43_A | 1.053 | 0.95 |
| 44_A | 48_A | 1.035 | 0.94 |
| 35_Q | 38_K | 1.034 | 0.94 |
| 30_A | 34_P | 1.022 | 0.93 |
| 49_T | 53_A | 1.018 | 0.93 |
| 63_Y | 67_S | 1.009 | 0.93 |
| 48_A | 52_I | 1.001 | 0.92 |
| 20_I | 36_Y | 1.001 | 0.92 |
| 41_R | 44_A | 1.000 | 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 | |
| 2hi2A | 1 | 0.8143 | 99 | 0.133 | Contact Map |
| 3sokA | 2 | 0.8286 | 99 | 0.144 | Contact Map |
| 1oqwA | 2 | 0.8286 | 98.8 | 0.179 | Contact Map |
| 2m7gA | 1 | 0.8286 | 98.8 | 0.201 | Contact Map |
| 3g20A | 2 | 0.5857 | 97.4 | 0.441 | Contact Map |
| 3gn9A | 3 | 0.4714 | 87.8 | 0.642 | Contact Map |
| 1t92A | 2 | 0.4714 | 86.7 | 0.648 | Contact Map |
| 2kepA | 1 | 0.4857 | 85.9 | 0.653 | Contact Map |
| 4noaA | 1 | 0.4571 | 83 | 0.665 | Contact Map |
| 2m3kA | 1 | 0.4857 | 80.8 | 0.672 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)