| Doc5 |
| ID: | 1466514919 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 96 (78) | ||
| Sequences: | 151 (144.3) | ||
| Seq/Len: | 1.936 | ||
| Nf(neff/√len): | 16.3 |
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: 1.936).
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 |
| 68_T | 71_S | 3.282 | 1.00 |
| 51_N | 88_G | 2.159 | 0.99 |
| 39_I | 76_V | 1.921 | 0.98 |
| 38_D | 76_V | 1.731 | 0.96 |
| 45_I | 82_I | 1.711 | 0.96 |
| 43_V | 80_Q | 1.693 | 0.96 |
| 74_V | 91_E | 1.486 | 0.90 |
| 31_A | 67_V | 1.475 | 0.90 |
| 46_M | 50_A | 1.429 | 0.88 |
| 28_P | 95_V | 1.396 | 0.86 |
| 90_V | 94_P | 1.367 | 0.84 |
| 66_D | 78_D | 1.337 | 0.82 |
| 43_V | 88_G | 1.314 | 0.81 |
| 68_T | 75_T | 1.311 | 0.81 |
| 40_S | 79_A | 1.307 | 0.80 |
| 36_I | 88_G | 1.301 | 0.80 |
| 46_M | 83_Q | 1.291 | 0.79 |
| 47_Q | 77_L | 1.254 | 0.76 |
| 92_L | 96_E | 1.250 | 0.76 |
| 40_S | 84_S | 1.246 | 0.76 |
| 39_I | 43_V | 1.246 | 0.76 |
| 30_D | 34_D | 1.219 | 0.74 |
| 79_A | 82_I | 1.188 | 0.71 |
| 68_T | 81_F | 1.175 | 0.70 |
| 76_V | 84_S | 1.175 | 0.70 |
| 31_A | 37_V | 1.174 | 0.70 |
| 41_D | 78_D | 1.144 | 0.67 |
| 30_D | 41_D | 1.142 | 0.66 |
| 41_D | 66_D | 1.141 | 0.66 |
| 72_D | 75_T | 1.092 | 0.61 |
| 25_Q | 75_T | 1.080 | 0.60 |
| 29_G | 78_D | 1.067 | 0.59 |
| 48_T | 75_T | 1.050 | 0.57 |
| 67_V | 82_I | 1.036 | 0.55 |
| 49_M | 87_L | 1.031 | 0.55 |
| 39_I | 87_L | 1.026 | 0.54 |
| 76_V | 83_Q | 1.024 | 0.54 |
| 60_K | 64_N | 1.022 | 0.54 |
| 29_G | 41_D | 1.022 | 0.54 |
| 47_Q | 84_S | 1.015 | 0.53 |
| 28_P | 74_V | 1.012 | 0.53 |
| 42_A | 83_Q | 1.007 | 0.52 |
| 37_V | 85_Y | 1.000 | 0.51 |
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 | |
| 4cj0A | 1 | 0.2083 | 99.8 | 0.108 | Contact Map |
| 2yikA | 1 | 0.1146 | 99.8 | 0.112 | Contact Map |
| 4uypB | 2 | 0.7396 | 99.8 | 0.133 | Contact Map |
| 4fl4A | 4 | 0.7083 | 99.8 | 0.142 | Contact Map |
| 4dh2B | 2 | 0.7292 | 99.7 | 0.16 | Contact Map |
| 2y3nB | 2 | 0.625 | 99.7 | 0.193 | Contact Map |
| 1daqA | 1 | 0.7188 | 99.7 | 0.202 | Contact Map |
| 2vn6B | 1 | 0.6667 | 99.6 | 0.226 | Contact Map |
| 2cclB | 2 | 0.6458 | 99.6 | 0.272 | Contact Map |
| 3ul4B | 1 | 0.6562 | 99.5 | 0.272 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)