| LEM2_CTD |
| ID: | 1492791615 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 106 (100) | ||
| Sequences: | 330 (225.6) | ||
| Seq/Len: | 3.300 | ||
| Nf(neff/√len): | 22.6 |
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: 3.300).
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 |
| 25_V | 78_I | 2.027 | 1.00 |
| 21_I | 67_A | 1.928 | 1.00 |
| 72_A | 91_L | 1.817 | 0.99 |
| 81_E | 94_R | 1.769 | 0.99 |
| 60_M | 91_L | 1.667 | 0.98 |
| 89_D | 94_R | 1.615 | 0.98 |
| 68_V | 93_W | 1.508 | 0.97 |
| 43_G | 46_H | 1.475 | 0.96 |
| 60_M | 67_A | 1.445 | 0.95 |
| 10_E | 66_R | 1.441 | 0.95 |
| 78_I | 93_W | 1.436 | 0.95 |
| 79_Q | 91_L | 1.431 | 0.95 |
| 67_A | 71_L | 1.410 | 0.94 |
| 14_M | 18_V | 1.407 | 0.94 |
| 18_V | 70_F | 1.395 | 0.94 |
| 83_H | 89_D | 1.369 | 0.93 |
| 47_V | 91_L | 1.344 | 0.92 |
| 83_H | 94_R | 1.343 | 0.92 |
| 32_W | 36_M | 1.338 | 0.92 |
| 47_V | 76_S | 1.326 | 0.92 |
| 52_I | 74_N | 1.304 | 0.91 |
| 70_F | 76_S | 1.289 | 0.90 |
| 24_V | 94_R | 1.268 | 0.89 |
| 16_E | 20_K | 1.218 | 0.86 |
| 48_R | 64_W | 1.217 | 0.86 |
| 27_D | 34_Q | 1.202 | 0.85 |
| 2_Y | 5_R | 1.197 | 0.85 |
| 28_H | 71_L | 1.193 | 0.85 |
| 42_V | 46_H | 1.181 | 0.84 |
| 52_I | 84_R | 1.172 | 0.83 |
| 2_Y | 6_K | 1.138 | 0.81 |
| 76_S | 95_W | 1.125 | 0.80 |
| 24_V | 47_V | 1.114 | 0.79 |
| 47_V | 74_N | 1.083 | 0.76 |
| 21_I | 54_P | 1.074 | 0.75 |
| 75_E | 79_Q | 1.073 | 0.75 |
| 11_E | 66_R | 1.071 | 0.75 |
| 67_A | 93_W | 1.071 | 0.75 |
| 42_V | 58_R | 1.064 | 0.74 |
| 37_E | 69_E | 1.052 | 0.73 |
| 75_E | 90_M | 1.050 | 0.73 |
| 25_V | 63_V | 1.046 | 0.72 |
| 26_Q | 29_Y | 1.044 | 0.72 |
| 16_E | 34_Q | 1.036 | 0.71 |
| 52_I | 60_M | 1.033 | 0.71 |
| 60_M | 76_S | 1.029 | 0.71 |
| 11_E | 39_Y | 1.023 | 0.70 |
| 87_G | 95_W | 1.022 | 0.70 |
| 75_E | 96_T | 1.020 | 0.70 |
| 79_Q | 93_W | 1.017 | 0.69 |
| 1_K | 22_I | 1.006 | 0.68 |
| 87_G | 93_W | 1.006 | 0.68 |
| 3_R | 7_L | 1.005 | 0.68 |
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 | |
| 2ch0A | 1 | 1 | 100 | 0.095 | Contact Map |
| 4gl6A | 2 | 0.3585 | 7.4 | 0.92 | Contact Map |
| 4l5gA | 2 | 0.6604 | 2.9 | 0.934 | Contact Map |
| 1hskA | 1 | 0.4151 | 2.8 | 0.935 | Contact Map |
| 4waiA | 4 | 0.3396 | 2.7 | 0.936 | Contact Map |
| 1jjrA | 1 | 0.2547 | 2.2 | 0.939 | Contact Map |
| 3pg5A | 4 | 0.1981 | 2.2 | 0.939 | Contact Map |
| 1wjwA | 1 | 0.3962 | 1.9 | 0.94 | Contact Map |
| 2jhpA | 1 | 0.9434 | 1.9 | 0.941 | Contact Map |
| 2nppB | 2 | 0.5 | 1.8 | 0.942 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)