| PhyR_rec_Coev_3 |
| ID: | 1482821622 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 136 (118) | ||
| Sequences: | 106877 (76115.3) | ||
| Seq/Len: | 905.737 | ||
| Nf(neff/√len): | 7007.0 |
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: 905.737).
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_A | 42_T | 2.820 | 1.00 |
| 25_A | 44_G | 2.504 | 1.00 |
| 29_G | 42_T | 2.413 | 1.00 |
| 18_V | 49_A | 2.402 | 1.00 |
| 41_G | 58_P | 2.286 | 1.00 |
| 63_L | 76_I | 2.082 | 1.00 |
| 47_A | 70_G | 1.971 | 1.00 |
| 108_Q | 122_A | 1.965 | 1.00 |
| 66_R | 94_F | 1.936 | 1.00 |
| 54_K | 83_V | 1.929 | 1.00 |
| 14_R | 38_I | 1.883 | 1.00 |
| 45_N | 70_G | 1.881 | 1.00 |
| 50_L | 79_R | 1.837 | 1.00 |
| 44_G | 48_E | 1.822 | 1.00 |
| 90_F | 106_L | 1.755 | 1.00 |
| 43_A | 52_L | 1.727 | 1.00 |
| 71_G | 79_R | 1.687 | 1.00 |
| 35_M | 120_Q | 1.681 | 1.00 |
| 14_R | 41_G | 1.673 | 1.00 |
| 46_E | 71_G | 1.666 | 1.00 |
| 77_A | 88_T | 1.662 | 1.00 |
| 81_K | 107_G | 1.600 | 1.00 |
| 31_L | 116_N | 1.583 | 1.00 |
| 16_M | 43_A | 1.565 | 1.00 |
| 72_S | 75_E | 1.522 | 1.00 |
| 41_G | 52_L | 1.463 | 1.00 |
| 45_N | 48_E | 1.405 | 0.99 |
| 29_G | 33_A | 1.371 | 0.99 |
| 71_G | 75_E | 1.348 | 0.99 |
| 79_R | 82_R | 1.328 | 0.99 |
| 50_L | 76_I | 1.317 | 0.99 |
| 65_V | 74_I | 1.282 | 0.99 |
| 14_R | 59_T | 1.263 | 0.99 |
| 108_Q | 125_R | 1.256 | 0.99 |
| 46_E | 76_I | 1.251 | 0.99 |
| 41_G | 56_E | 1.248 | 0.99 |
| 53_L | 80_L | 1.228 | 0.98 |
| 78_R | 104_G | 1.215 | 0.98 |
| 13_Q | 37_H | 1.212 | 0.98 |
| 79_R | 83_V | 1.177 | 0.98 |
| 77_A | 90_F | 1.170 | 0.97 |
| 61_A | 86_L | 1.164 | 0.97 |
| 63_L | 77_A | 1.156 | 0.97 |
| 20_D | 64_D | 1.149 | 0.97 |
| 52_L | 58_P | 1.137 | 0.97 |
| 14_R | 56_E | 1.137 | 0.97 |
| 122_A | 125_R | 1.131 | 0.97 |
| 91_V | 114_F | 1.127 | 0.97 |
| 107_G | 126_A | 1.102 | 0.96 |
| 13_Q | 127_I | 1.099 | 0.96 |
| 16_M | 49_A | 1.093 | 0.96 |
| 49_A | 76_I | 1.093 | 0.96 |
| 43_A | 49_A | 1.092 | 0.96 |
| 47_A | 51_A | 1.067 | 0.95 |
| 118_G | 122_A | 1.063 | 0.95 |
| 63_L | 88_T | 1.059 | 0.95 |
| 47_A | 71_G | 1.057 | 0.95 |
| 61_A | 88_T | 1.052 | 0.95 |
| 15_V | 37_H | 1.045 | 0.94 |
| 65_V | 90_F | 1.039 | 0.94 |
| 90_F | 101_R | 1.035 | 0.94 |
| 21_N | 24_L | 1.032 | 0.94 |
| 26_L | 29_G | 1.031 | 0.94 |
| 12_V | 38_I | 1.019 | 0.93 |
| 52_L | 55_A | 1.013 | 0.93 |
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 | |
| 4g97A | 1 | 1 | 99.3 | -0.106 | Contact Map |
| 3n0rA | 1 | 0.9706 | 99.3 | -0.092 | Contact Map |
| 2gwrA | 1 | 0.9265 | 99.1 | -0.039 | Contact Map |
| 3q9sA | 1 | 0.9044 | 99.1 | -0.029 | Contact Map |
| 4qicA | 2 | 0 | 99.1 | -0.025 | Contact Map |
| 2oqrA | 1 | 0.9044 | 99.1 | -0.021 | Contact Map |
| 4kfcA | 2 | 0.9044 | 99.1 | -0.01 | Contact Map |
| 4b09A | 12 | 0.8382 | 99.1 | -0.003 | Contact Map |
| 3rqiA | 1 | 0.8971 | 99 | 0 | Contact Map |
| 1s8nA | 1 | 0.9265 | 99 | 0.002 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)