| RRE-from INTERPRO |
| ID: | 1485467525 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 116 (114) | ||
| Sequences: | 325 (260.4) | ||
| Seq/Len: | 2.851 | ||
| Nf(neff/√len): | 24.4 |
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: 2.851).
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 |
| 80_I | 94_P | 2.697 | 1.00 |
| 25_W | 68_R | 2.578 | 1.00 |
| 66_V | 79_I | 2.210 | 1.00 |
| 88_Q | 92_N | 1.882 | 0.99 |
| 62_H | 83_L | 1.692 | 0.98 |
| 36_R | 43_R | 1.596 | 0.97 |
| 40_D | 43_R | 1.570 | 0.97 |
| 30_A | 64_T | 1.554 | 0.96 |
| 74_R | 82_L | 1.518 | 0.96 |
| 69_L | 82_L | 1.479 | 0.95 |
| 66_V | 83_L | 1.447 | 0.94 |
| 99_T | 102_M | 1.431 | 0.93 |
| 45_F | 49_K | 1.415 | 0.93 |
| 43_R | 51_M | 1.412 | 0.93 |
| 36_R | 55_I | 1.408 | 0.93 |
| 46_L | 51_M | 1.376 | 0.92 |
| 80_I | 95_S | 1.355 | 0.91 |
| 40_D | 47_L | 1.339 | 0.90 |
| 41_W | 45_F | 1.333 | 0.90 |
| 80_I | 97_V | 1.327 | 0.89 |
| 6_G | 115_E | 1.315 | 0.89 |
| 18_C | 109_F | 1.309 | 0.89 |
| 70_I | 79_I | 1.267 | 0.86 |
| 49_K | 57_V | 1.260 | 0.86 |
| 17_Q | 67_W | 1.259 | 0.86 |
| 43_R | 47_L | 1.248 | 0.85 |
| 83_L | 101_I | 1.226 | 0.84 |
| 74_R | 79_I | 1.202 | 0.82 |
| 3_D | 6_G | 1.201 | 0.82 |
| 15_P | 67_W | 1.197 | 0.82 |
| 14_V | 70_I | 1.186 | 0.81 |
| 44_R | 112_L | 1.179 | 0.80 |
| 16_V | 113_K | 1.174 | 0.80 |
| 33_S | 56_H | 1.154 | 0.78 |
| 42_M | 48_P | 1.146 | 0.78 |
| 41_W | 44_R | 1.133 | 0.77 |
| 5_K | 116_S | 1.129 | 0.76 |
| 17_Q | 70_I | 1.127 | 0.76 |
| 65_A | 83_L | 1.123 | 0.76 |
| 25_W | 28_E | 1.113 | 0.75 |
| 4_T | 116_S | 1.109 | 0.74 |
| 102_M | 106_K | 1.096 | 0.73 |
| 3_D | 115_E | 1.092 | 0.73 |
| 53_A | 90_E | 1.090 | 0.73 |
| 111_Q | 114_V | 1.062 | 0.70 |
| 35_P | 56_H | 1.053 | 0.69 |
| 43_R | 46_L | 1.049 | 0.68 |
| 100_Y | 112_L | 1.049 | 0.68 |
| 4_T | 115_E | 1.049 | 0.68 |
| 6_G | 116_S | 1.041 | 0.68 |
| 39_Y | 43_R | 1.032 | 0.67 |
| 32_L | 69_L | 1.030 | 0.66 |
| 44_R | 53_A | 1.028 | 0.66 |
| 72_G | 79_I | 1.025 | 0.66 |
| 40_D | 51_M | 1.024 | 0.66 |
| 52_S | 92_N | 1.018 | 0.65 |
| 42_M | 47_L | 1.016 | 0.65 |
| 40_D | 46_L | 1.013 | 0.65 |
| 2_S | 5_K | 1.010 | 0.64 |
| 59_L | 63_G | 1.010 | 0.64 |
| 39_Y | 46_L | 1.006 | 0.64 |
| 101_I | 112_L | 1.005 | 0.64 |
| 80_I | 83_L | 1.004 | 0.64 |
| 57_V | 90_E | 1.003 | 0.63 |
| 93_Y | 96_R | 1.002 | 0.63 |
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 | |
| 3g2bA | 1 | 0.75 | 99.4 | 0.542 | Contact Map |
| 4wd9A | 2 | 0.8534 | 83.2 | 0.851 | Contact Map |
| 2co5A | 2 | 0.5517 | 43.5 | 0.887 | Contact Map |
| 3h5nA | 4 | 0.681 | 43.4 | 0.887 | Contact Map |
| 4v1tA | 2 | 0.7155 | 40.9 | 0.889 | Contact Map |
| 4esjA | 2 | 0.8448 | 27.2 | 0.899 | Contact Map |
| 2dqlA | 2 | 0.6638 | 26.4 | 0.9 | Contact Map |
| 3l09A | 4 | 0.6466 | 25.5 | 0.901 | Contact Map |
| 2bl8A | 3 | 0.5517 | 18.8 | 0.906 | Contact Map |
| 2mh2A | 1 | 0.4828 | 17.7 | 0.908 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)