| Precursor RRE |
| ID: | 1500592901 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (130) | ||
| Sequences: | 304 (261.4) | ||
| Seq/Len: | 2.338 | ||
| Nf(neff/√len): | 22.9 |
Jackhmmer Results: (2016_04)
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: 2.338).
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 |
| 13_Y | 16_P | 2.861 | 1.00 |
| 13_Y | 28_T | 2.037 | 0.99 |
| 107_I | 112_A | 1.946 | 0.99 |
| 35_G | 38_N | 1.829 | 0.98 |
| 20_E | 73_V | 1.804 | 0.98 |
| 18_V | 128_V | 1.785 | 0.98 |
| 64_I | 82_A | 1.604 | 0.96 |
| 92_G | 97_A | 1.476 | 0.92 |
| 75_W | 112_A | 1.449 | 0.91 |
| 34_W | 38_N | 1.443 | 0.91 |
| 109_E | 113_R | 1.402 | 0.90 |
| 41_S | 44_R | 1.349 | 0.87 |
| 22_G | 28_T | 1.333 | 0.86 |
| 34_W | 41_S | 1.332 | 0.86 |
| 38_N | 41_S | 1.326 | 0.86 |
| 13_Y | 115_D | 1.326 | 0.86 |
| 13_Y | 22_G | 1.316 | 0.85 |
| 36_F | 44_R | 1.308 | 0.85 |
| 112_A | 116_V | 1.273 | 0.83 |
| 21_M | 27_V | 1.261 | 0.82 |
| 97_A | 120_I | 1.254 | 0.81 |
| 113_R | 117_E | 1.234 | 0.80 |
| 37_E | 46_C | 1.207 | 0.78 |
| 93_D | 96_V | 1.206 | 0.78 |
| 83_E | 129_L | 1.200 | 0.77 |
| 75_W | 126_V | 1.199 | 0.77 |
| 60_T | 63_G | 1.171 | 0.75 |
| 37_E | 44_R | 1.169 | 0.74 |
| 55_I | 66_L | 1.154 | 0.73 |
| 29_L | 38_N | 1.150 | 0.73 |
| 123_L | 128_V | 1.139 | 0.72 |
| 37_E | 40_W | 1.135 | 0.71 |
| 88_L | 112_A | 1.131 | 0.71 |
| 82_A | 86_R | 1.129 | 0.71 |
| 123_L | 129_L | 1.128 | 0.71 |
| 13_Y | 24_F | 1.127 | 0.71 |
| 65_V | 72_G | 1.126 | 0.70 |
| 83_E | 104_R | 1.108 | 0.69 |
| 50_I | 95_D | 1.105 | 0.68 |
| 75_W | 85_L | 1.103 | 0.68 |
| 94_R | 120_I | 1.099 | 0.68 |
| 37_E | 41_S | 1.093 | 0.67 |
| 99_A | 103_D | 1.092 | 0.67 |
| 65_V | 74_Y | 1.092 | 0.67 |
| 57_S | 64_I | 1.091 | 0.67 |
| 86_R | 90_E | 1.086 | 0.66 |
| 22_G | 27_V | 1.085 | 0.66 |
| 16_P | 28_T | 1.085 | 0.66 |
| 51_D | 85_L | 1.080 | 0.66 |
| 121_R | 130_R | 1.079 | 0.66 |
| 101_I | 116_V | 1.074 | 0.65 |
| 115_D | 123_L | 1.072 | 0.65 |
| 25_S | 39_D | 1.070 | 0.65 |
| 71_K | 82_A | 1.069 | 0.65 |
| 67_L | 123_L | 1.061 | 0.64 |
| 62_D | 105_Y | 1.051 | 0.63 |
| 39_D | 46_C | 1.046 | 0.62 |
| 24_F | 28_T | 1.042 | 0.62 |
| 39_D | 45_V | 1.039 | 0.61 |
| 31_R | 40_W | 1.039 | 0.61 |
| 76_H | 85_L | 1.037 | 0.61 |
| 78_N | 115_D | 1.025 | 0.60 |
| 59_E | 64_I | 1.023 | 0.60 |
| 117_E | 121_R | 1.022 | 0.60 |
| 68_D | 71_K | 1.020 | 0.59 |
| 86_R | 120_I | 1.019 | 0.59 |
| 40_W | 44_R | 1.019 | 0.59 |
| 2_D | 5_K | 1.018 | 0.59 |
| 3_E | 7_G | 1.016 | 0.59 |
| 30_G | 40_W | 1.008 | 0.58 |
| 30_G | 39_D | 1.008 | 0.58 |
| 68_D | 78_N | 1.002 | 0.57 |
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 | 0.6718 | 99.2 | 0.533 | Contact Map |
| 3h5nA | 4 | 0.5725 | 85 | 0.829 | Contact Map |
| 4v1tA | 2 | 0.6031 | 83.4 | 0.832 | Contact Map |
| 4a0zA | 2 | 0.3969 | 33.3 | 0.881 | Contact Map |
| 4un1A | 2 | 0.3969 | 24.9 | 0.889 | Contact Map |
| 2gqqA | 4 | 0.4046 | 24 | 0.889 | Contact Map |
| 2cfxA | 8 | 0.3893 | 22.4 | 0.891 | Contact Map |
| 1i1gA | 2 | 0.374 | 19.1 | 0.894 | Contact Map |
| 2dk5A | 1 | 0.5115 | 19.1 | 0.894 | Contact Map |
| 1p6rA | 1 | 0.4351 | 18.8 | 0.895 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)