| rte2 |
| ID: | 1491986282 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 107 (107) | ||
| Sequences: | 328 (215.8) | ||
| Seq/Len: | 3.065 | ||
| Nf(neff/√len): | 20.9 |
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: 3.065).
- Analysis in progress
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 |
| 33_F | 67_A | 2.971 | 1.00 |
| 29_A | 70_L | 2.335 | 1.00 |
| 36_P | 62_I | 1.989 | 1.00 |
| 58_F | 62_I | 1.848 | 0.99 |
| 25_D | 91_K | 1.825 | 0.99 |
| 71_I | 90_A | 1.811 | 0.99 |
| 74_W | 79_H | 1.766 | 0.99 |
| 78_T | 81_R | 1.717 | 0.99 |
| 21_Q | 88_T | 1.695 | 0.98 |
| 72_N | 91_K | 1.686 | 0.98 |
| 77_T | 81_R | 1.617 | 0.98 |
| 20_Y | 88_T | 1.530 | 0.96 |
| 62_I | 65_C | 1.523 | 0.96 |
| 54_V | 97_V | 1.440 | 0.94 |
| 51_Y | 86_V | 1.384 | 0.93 |
| 20_Y | 92_V | 1.373 | 0.92 |
| 43_V | 55_L | 1.332 | 0.91 |
| 94_T | 98_S | 1.284 | 0.89 |
| 12_P | 16_L | 1.267 | 0.88 |
| 9_P | 12_P | 1.257 | 0.87 |
| 52_R | 64_L | 1.256 | 0.87 |
| 61_F | 69_H | 1.216 | 0.85 |
| 42_F | 51_Y | 1.196 | 0.83 |
| 9_P | 87_M | 1.196 | 0.83 |
| 56_V | 89_T | 1.171 | 0.82 |
| 39_L | 50_P | 1.171 | 0.82 |
| 31_A | 41_Y | 1.153 | 0.80 |
| 32_Y | 69_H | 1.131 | 0.78 |
| 43_V | 52_R | 1.130 | 0.78 |
| 54_V | 64_L | 1.129 | 0.78 |
| 18_M | 76_F | 1.127 | 0.78 |
| 53_W | 57_Q | 1.119 | 0.77 |
| 59_G | 63_V | 1.107 | 0.76 |
| 10_Q | 17_L | 1.103 | 0.76 |
| 47_A | 59_G | 1.089 | 0.75 |
| 62_I | 94_T | 1.087 | 0.74 |
| 69_H | 98_S | 1.082 | 0.74 |
| 50_P | 59_G | 1.079 | 0.74 |
| 15_E | 84_A | 1.070 | 0.73 |
| 28_I | 95_A | 1.066 | 0.72 |
| 3_V | 6_C | 1.064 | 0.72 |
| 34_S | 102_A | 1.063 | 0.72 |
| 62_I | 68_T | 1.062 | 0.72 |
| 98_S | 101_T | 1.061 | 0.72 |
| 37_L | 97_V | 1.058 | 0.72 |
| 62_I | 69_H | 1.056 | 0.71 |
| 25_D | 101_T | 1.055 | 0.71 |
| 34_S | 44_K | 1.050 | 0.71 |
| 9_P | 73_L | 1.044 | 0.70 |
| 75_T | 105_L | 1.044 | 0.70 |
| 36_P | 65_C | 1.041 | 0.70 |
| 60_A | 97_V | 1.039 | 0.70 |
| 36_P | 66_G | 1.033 | 0.69 |
| 13_A | 68_T | 1.032 | 0.69 |
| 39_L | 55_L | 1.014 | 0.67 |
| 100_A | 104_M | 1.012 | 0.67 |
| 30_I | 70_L | 1.012 | 0.67 |
| 53_W | 59_G | 1.005 | 0.66 |
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 | |
| 2hi7B | 1 | 0.1869 | 1.9 | 0.938 | Contact Map |
| 1v54A | 2 | 0.8879 | 1.7 | 0.94 | Contact Map |
| 1fftA | 2 | 0.8972 | 1.5 | 0.941 | Contact Map |
| 2kdrX | 1 | 0.1963 | 1.3 | 0.944 | Contact Map |
| 2yevA | 2 | 0.8972 | 1.2 | 0.945 | Contact Map |
| 4nuxA | 1 | 0.6168 | 1 | 0.948 | Contact Map |
| 2mpnA | 2 | 0.5421 | 0.8 | 0.95 | Contact Map |
| 3vbcA | 1 | 0.6355 | 0.8 | 0.95 | Contact Map |
| 2lq0A | 1 | 0.2336 | 0.8 | 0.951 | Contact Map |
| 1xqoA | 1 | 0.4019 | 0.8 | 0.951 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)