| T0824 |
| ID: | 1403210945 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (107) | ||
| Sequences: | 263 (231) | ||
| Seq/Len: | 2.458 | ||
| Nf(neff/√len): | 22.3 |
Jackhmmer Results: (2014_04_16)
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: 2.458).
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 | 3.935 | 1.00 |
| 45_R | 66_A | 2.933 | 1.00 |
| 59_D | 86_R | 2.877 | 1.00 |
| 34_C | 63_W | 2.388 | 1.00 |
| 15_Y | 87_G | 1.981 | 0.99 |
| 21_H | 76_S | 1.978 | 0.99 |
| 67_M | 96_L | 1.869 | 0.99 |
| 25_A | 63_W | 1.863 | 0.99 |
| 18_T | 80_V | 1.801 | 0.98 |
| 49_L | 60_R | 1.784 | 0.98 |
| 68_C | 105_I | 1.705 | 0.98 |
| 92_V | 107_F | 1.698 | 0.97 |
| 63_W | 107_F | 1.628 | 0.96 |
| 12_A | 23_S | 1.543 | 0.95 |
| 72_G | 75_A | 1.512 | 0.94 |
| 85_N | 88_A | 1.488 | 0.93 |
| 12_A | 19_G | 1.471 | 0.93 |
| 59_D | 85_N | 1.386 | 0.90 |
| 80_V | 84_D | 1.385 | 0.90 |
| 42_D | 53_P | 1.385 | 0.90 |
| 60_R | 79_Y | 1.357 | 0.88 |
| 59_D | 90_S | 1.314 | 0.86 |
| 65_M | 68_C | 1.289 | 0.85 |
| 17_E | 84_D | 1.278 | 0.84 |
| 23_S | 79_Y | 1.244 | 0.82 |
| 50_K | 56_P | 1.219 | 0.80 |
| 86_R | 90_S | 1.181 | 0.77 |
| 18_T | 88_A | 1.174 | 0.76 |
| 18_T | 84_D | 1.174 | 0.76 |
| 67_M | 92_V | 1.170 | 0.76 |
| 33_V | 70_E | 1.158 | 0.75 |
| 106_L | 109_V | 1.141 | 0.73 |
| 28_A | 78_R | 1.127 | 0.72 |
| 25_A | 89_G | 1.126 | 0.72 |
| 80_V | 88_A | 1.121 | 0.71 |
| 48_S | 75_A | 1.108 | 0.70 |
| 34_C | 65_M | 1.102 | 0.70 |
| 11_P | 23_S | 1.073 | 0.67 |
| 24_D | 28_A | 1.066 | 0.66 |
| 20_A | 24_D | 1.065 | 0.66 |
| 10_F | 68_C | 1.045 | 0.64 |
| 60_R | 65_M | 1.024 | 0.61 |
| 94_N | 109_V | 1.022 | 0.61 |
| 87_G | 90_S | 1.006 | 0.59 |
| 37_E | 44_R | 1.005 | 0.59 |
| 32_D | 106_L | 1.004 | 0.59 |
| 58_F | 79_Y | 1.000 | 0.59 |
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 | 7.6 | 0.93 | Contact Map |
| 4iykA | 1 | 0.3727 | 4.6 | 0.936 | Contact Map |
| 4l0kA | 4 | 0.6818 | 3.4 | 0.94 | Contact Map |
| 1q2fA | 1 | 0.2727 | 3.4 | 0.941 | Contact Map |
| 2plxB | 1 | 0.2364 | 3 | 0.942 | Contact Map |
| 2xuvA | 4 | 0.3727 | 2.8 | 0.943 | Contact Map |
| 3bdlA | 1 | 0.2091 | 2.4 | 0.945 | Contact Map |
| 3vgfA | 1 | 0.4909 | 2.4 | 0.945 | Contact Map |
| 4nj5A | 1 | 0.3364 | 2.2 | 0.946 | Contact Map |
| 1dj8A | 6 | 0.4091 | 2 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)