| kaib7-94 |
| ID: | 1479601436 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (88) | ||
| Sequences: | 321 (239.5) | ||
| Seq/Len: | 3.648 | ||
| Nf(neff/√len): | 25.5 |
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: 3.648).
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 |
| 23_N | 27_E | 1.989 | 1.00 |
| 26_L | 30_F | 1.813 | 0.99 |
| 23_N | 36_L | 1.736 | 0.99 |
| 1_T | 35_A | 1.655 | 0.99 |
| 61_K | 64_P | 1.584 | 0.98 |
| 41_V | 56_T | 1.573 | 0.98 |
| 8_V | 25_I | 1.539 | 0.98 |
| 48_A | 68_R | 1.432 | 0.96 |
| 4_L | 83_G | 1.401 | 0.95 |
| 60_A | 69_R | 1.391 | 0.95 |
| 74_L | 84_L | 1.375 | 0.94 |
| 15_S | 76_N | 1.353 | 0.94 |
| 60_A | 74_L | 1.353 | 0.94 |
| 63_L | 85_D | 1.332 | 0.93 |
| 59_L | 70_I | 1.322 | 0.93 |
| 4_L | 81_L | 1.313 | 0.92 |
| 30_F | 40_D | 1.306 | 0.92 |
| 46_Q | 50_E | 1.303 | 0.92 |
| 7_Y | 51_D | 1.284 | 0.91 |
| 65_P | 85_D | 1.283 | 0.91 |
| 25_I | 80_V | 1.252 | 0.90 |
| 9_A | 42_L | 1.224 | 0.89 |
| 11_N | 41_V | 1.218 | 0.88 |
| 5_K | 37_K | 1.208 | 0.88 |
| 61_K | 85_D | 1.208 | 0.88 |
| 18_A | 32_G | 1.188 | 0.86 |
| 44_N | 47_L | 1.180 | 0.86 |
| 1_T | 88_Y | 1.154 | 0.84 |
| 21_T | 75_S | 1.135 | 0.83 |
| 29_E | 56_T | 1.131 | 0.83 |
| 27_E | 34_Y | 1.114 | 0.81 |
| 73_D | 84_L | 1.094 | 0.80 |
| 6_L | 59_L | 1.092 | 0.79 |
| 26_L | 33_V | 1.082 | 0.79 |
| 51_D | 60_A | 1.076 | 0.78 |
| 50_E | 87_L | 1.065 | 0.77 |
| 51_D | 62_V | 1.062 | 0.77 |
| 63_L | 82_I | 1.058 | 0.76 |
| 42_L | 56_T | 1.055 | 0.76 |
| 80_V | 84_L | 1.050 | 0.76 |
| 2_Y | 34_Y | 1.045 | 0.75 |
| 27_E | 36_L | 1.038 | 0.74 |
| 54_L | 75_S | 1.035 | 0.74 |
| 38_V | 49_E | 1.028 | 0.73 |
| 7_Y | 86_L | 1.015 | 0.72 |
| 39_I | 71_I | 1.012 | 0.72 |
| 77_R | 80_V | 1.005 | 0.71 |
| 67_V | 85_D | 1.001 | 0.71 |
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 | |
| 1t4yA | 1 | 0.9432 | 99.9 | 0.273 | Contact Map |
| 4kunA | 2 | 0.9886 | 99.8 | 0.404 | Contact Map |
| 1wwjA | 4 | 1 | 99.8 | 0.435 | Contact Map |
| 1iloA | 1 | 0.875 | 93.9 | 0.824 | Contact Map |
| 1qgvA | 1 | 0.9659 | 93.8 | 0.825 | Contact Map |
| 4cdoA | 2 | 0.9886 | 93.7 | 0.826 | Contact Map |
| 2av4A | 1 | 0.9886 | 93.4 | 0.828 | Contact Map |
| 1fo5A | 1 | 0.9432 | 93.3 | 0.828 | Contact Map |
| 1nhoA | 1 | 0.9432 | 91.6 | 0.837 | Contact Map |
| 2fgxA | 1 | 0.875 | 91.6 | 0.837 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)