| Tim10 |
| ID: | 1496341506 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 93 (90) | ||
| Sequences: | 526 (324.8) | ||
| Seq/Len: | 5.844 | ||
| Nf(neff/√len): | 34.2 |
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: 5.844).
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 |
| 40_C | 65_C | 2.528 | 1.00 |
| 31_D | 35_K | 2.168 | 1.00 |
| 11_P | 15_S | 1.650 | 1.00 |
| 58_E | 64_R | 1.571 | 0.99 |
| 69_Y | 76_V | 1.527 | 0.99 |
| 21_A | 77_G | 1.525 | 0.99 |
| 13_L | 16_Q | 1.518 | 0.99 |
| 27_D | 33_F | 1.505 | 0.99 |
| 57_N | 60_S | 1.463 | 0.99 |
| 25_E | 31_D | 1.455 | 0.99 |
| 45_I | 54_L | 1.419 | 0.98 |
| 70_F | 73_N | 1.407 | 0.98 |
| 39_N | 43_K | 1.399 | 0.98 |
| 23_E | 76_V | 1.397 | 0.98 |
| 7_G | 10_Q | 1.379 | 0.98 |
| 26_L | 30_T | 1.307 | 0.97 |
| 36_L | 73_N | 1.265 | 0.96 |
| 22_A | 34_N | 1.242 | 0.95 |
| 28_L | 70_F | 1.235 | 0.95 |
| 25_E | 63_D | 1.234 | 0.95 |
| 11_P | 14_S | 1.226 | 0.95 |
| 86_S | 89_A | 1.226 | 0.95 |
| 31_D | 43_K | 1.220 | 0.95 |
| 2_S | 5_G | 1.216 | 0.95 |
| 34_N | 66_V | 1.211 | 0.94 |
| 30_T | 78_E | 1.199 | 0.94 |
| 1_M | 4_L | 1.167 | 0.93 |
| 88_N | 91_G | 1.157 | 0.92 |
| 17_Q | 23_E | 1.144 | 0.92 |
| 30_T | 75_Q | 1.141 | 0.92 |
| 26_L | 69_Y | 1.122 | 0.91 |
| 45_I | 72_T | 1.113 | 0.90 |
| 5_G | 8_G | 1.099 | 0.90 |
| 22_A | 77_G | 1.095 | 0.89 |
| 32_M | 70_F | 1.076 | 0.88 |
| 56_K | 60_S | 1.068 | 0.88 |
| 11_P | 16_Q | 1.055 | 0.87 |
| 16_Q | 20_Q | 1.050 | 0.87 |
| 38_N | 51_E | 1.047 | 0.86 |
| 8_G | 11_P | 1.046 | 0.86 |
| 37_V | 41_Y | 1.044 | 0.86 |
| 36_L | 66_V | 1.044 | 0.86 |
| 26_L | 68_K | 1.041 | 0.86 |
| 64_R | 68_K | 1.029 | 0.85 |
| 63_D | 67_A | 1.024 | 0.85 |
| 3_F | 8_G | 1.022 | 0.85 |
| 36_L | 59_S | 1.017 | 0.84 |
| 22_A | 35_K | 1.008 | 0.84 |
| 7_G | 12_Q | 1.002 | 0.83 |
| 20_Q | 64_R | 1.000 | 0.83 |
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 | |
| 3dxrB | 1 | 0.7419 | 99.9 | 0.113 | Contact Map |
| 2bskB | 3 | 0.8817 | 99.8 | 0.295 | Contact Map |
| 3dxrA | 1 | 0.7419 | 99.8 | 0.319 | Contact Map |
| 3cjhB | 6 | 0.6344 | 99.8 | 0.326 | Contact Map |
| 2bskA | 3 | 0.7742 | 99.8 | 0.353 | Contact Map |
| 3cjhA | 6 | 0.5806 | 99.7 | 0.379 | Contact Map |
| 2plxB | 1 | 0.2796 | 6.1 | 0.919 | Contact Map |
| 3j8eG | 4 | 0.8387 | 4.1 | 0.925 | Contact Map |
| 2cmyB | 1 | 0.2258 | 2.5 | 0.933 | Contact Map |
| 2dhyA | 1 | 0.7204 | 2.2 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)