| T0824 |
| ID: | 1423535876 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (106) | ||
| Sequences: | 327 (274.7) | ||
| Seq/Len: | 3.085 | ||
| Nf(neff/√len): | 26.7 |
Jackhmmer Results: (2015_01_07)
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: 3.085).
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 |
| 24_D | 78_R | 4.477 | 1.00 |
| 59_D | 86_R | 3.098 | 1.00 |
| 63_W | 107_F | 2.179 | 1.00 |
| 18_T | 80_V | 1.987 | 1.00 |
| 67_M | 96_L | 1.931 | 1.00 |
| 49_L | 52_I | 1.884 | 0.99 |
| 18_T | 84_D | 1.846 | 0.99 |
| 21_H | 76_S | 1.804 | 0.99 |
| 92_V | 96_L | 1.778 | 0.99 |
| 45_R | 66_A | 1.759 | 0.99 |
| 17_E | 84_D | 1.749 | 0.99 |
| 49_L | 60_R | 1.715 | 0.99 |
| 68_C | 105_I | 1.675 | 0.98 |
| 12_A | 23_S | 1.617 | 0.98 |
| 34_C | 63_W | 1.612 | 0.98 |
| 33_V | 70_E | 1.589 | 0.97 |
| 92_V | 107_F | 1.546 | 0.97 |
| 15_Y | 87_G | 1.544 | 0.97 |
| 67_M | 92_V | 1.517 | 0.96 |
| 100_A | 103_T | 1.510 | 0.96 |
| 72_G | 75_A | 1.473 | 0.95 |
| 17_E | 81_S | 1.460 | 0.95 |
| 48_S | 72_G | 1.425 | 0.94 |
| 86_R | 90_S | 1.419 | 0.94 |
| 8_L | 20_A | 1.351 | 0.92 |
| 34_C | 65_M | 1.326 | 0.91 |
| 21_H | 25_A | 1.320 | 0.90 |
| 49_L | 59_D | 1.316 | 0.90 |
| 58_F | 79_Y | 1.293 | 0.89 |
| 43_K | 46_Q | 1.263 | 0.88 |
| 47_E | 50_K | 1.219 | 0.85 |
| 70_E | 82_S | 1.215 | 0.85 |
| 18_T | 88_A | 1.205 | 0.84 |
| 34_C | 98_G | 1.205 | 0.84 |
| 80_V | 84_D | 1.137 | 0.79 |
| 60_R | 65_M | 1.099 | 0.76 |
| 23_S | 79_Y | 1.089 | 0.75 |
| 48_S | 71_G | 1.073 | 0.73 |
| 12_A | 19_G | 1.068 | 0.73 |
| 10_F | 91_W | 1.060 | 0.72 |
| 59_D | 90_S | 1.060 | 0.72 |
| 41_A | 45_R | 1.040 | 0.70 |
| 22_I | 88_A | 1.024 | 0.68 |
| 33_V | 104_R | 1.022 | 0.68 |
| 24_D | 27_K | 1.020 | 0.68 |
| 15_Y | 91_W | 1.018 | 0.67 |
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 | |
| 2cmyB | 1 | 0.1909 | 8.4 | 0.935 | Contact Map |
| 3bdlA | 1 | 0.2091 | 7.8 | 0.936 | Contact Map |
| 3a0yA | 2 | 0.9455 | 6.5 | 0.938 | Contact Map |
| 1v5nA | 1 | 0.7 | 4.7 | 0.942 | Contact Map |
| 2plxB | 1 | 0.2364 | 3.7 | 0.945 | Contact Map |
| 1olgA | 4 | 0.1364 | 3.5 | 0.945 | Contact Map |
| 4c2mA | 2 | 0.8636 | 3.3 | 0.946 | Contact Map |
| 1q2fA | 1 | 0.2727 | 2.8 | 0.948 | Contact Map |
| 4wbdA | 1 | 0.4 | 2.8 | 0.948 | Contact Map |
| 3a0rA | 1 | 0.8909 | 2.8 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)