| Precursor RRE |
| ID: | 1515795750 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 130 (125) | ||
| Sequences: | 308 (267) | ||
| Seq/Len: | 2.464 | ||
| Nf(neff/√len): | 23.9 |
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: 2.464).
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 |
| 6_Y | 9_P | 2.967 | 1.00 |
| 6_Y | 21_T | 2.062 | 1.00 |
| 106_V | 111_A | 1.956 | 0.99 |
| 26_A | 29_G | 1.838 | 0.99 |
| 13_K | 72_E | 1.838 | 0.99 |
| 11_L | 127_M | 1.723 | 0.98 |
| 63_M | 81_A | 1.568 | 0.95 |
| 25_T | 29_G | 1.510 | 0.94 |
| 108_R | 112_E | 1.432 | 0.92 |
| 91_H | 96_V | 1.424 | 0.91 |
| 74_W | 111_A | 1.377 | 0.89 |
| 6_Y | 15_G | 1.376 | 0.89 |
| 29_G | 32_L | 1.376 | 0.89 |
| 25_T | 32_L | 1.342 | 0.88 |
| 32_L | 35_V | 1.337 | 0.87 |
| 37_P | 40_I | 1.320 | 0.87 |
| 6_Y | 114_D | 1.310 | 0.86 |
| 14_V | 20_A | 1.300 | 0.85 |
| 15_G | 21_T | 1.299 | 0.85 |
| 27_E | 35_V | 1.281 | 0.84 |
| 111_A | 115_I | 1.275 | 0.84 |
| 112_E | 116_A | 1.236 | 0.81 |
| 87_L | 111_A | 1.224 | 0.80 |
| 96_V | 119_V | 1.219 | 0.80 |
| 9_P | 21_T | 1.188 | 0.77 |
| 59_T | 62_G | 1.184 | 0.77 |
| 81_A | 85_Q | 1.162 | 0.75 |
| 28_W | 37_P | 1.156 | 0.75 |
| 74_W | 125_N | 1.152 | 0.74 |
| 120_T | 129_L | 1.147 | 0.74 |
| 6_Y | 17_F | 1.145 | 0.74 |
| 28_W | 35_V | 1.137 | 0.73 |
| 54_I | 65_L | 1.136 | 0.73 |
| 122_L | 127_M | 1.136 | 0.73 |
| 58_Q | 63_M | 1.132 | 0.73 |
| 98_Q | 102_S | 1.129 | 0.72 |
| 56_V | 63_M | 1.127 | 0.72 |
| 82_L | 128_A | 1.110 | 0.70 |
| 61_Y | 104_Y | 1.103 | 0.70 |
| 67_D | 70_S | 1.100 | 0.69 |
| 28_W | 31_E | 1.100 | 0.69 |
| 92_S | 95_D | 1.096 | 0.69 |
| 4_K | 103_E | 1.082 | 0.68 |
| 74_W | 84_V | 1.082 | 0.68 |
| 122_L | 128_A | 1.082 | 0.68 |
| 15_G | 20_A | 1.078 | 0.67 |
| 28_W | 32_L | 1.076 | 0.67 |
| 116_A | 120_T | 1.073 | 0.67 |
| 6_Y | 16_E | 1.066 | 0.66 |
| 64_V | 71_G | 1.063 | 0.66 |
| 100_L | 115_I | 1.060 | 0.65 |
| 50_L | 84_V | 1.059 | 0.65 |
| 66_L | 122_L | 1.058 | 0.65 |
| 93_P | 119_V | 1.051 | 0.64 |
| 18_K | 30_L | 1.050 | 0.64 |
| 64_V | 73_Y | 1.050 | 0.64 |
| 30_L | 40_I | 1.048 | 0.64 |
| 22_G | 31_E | 1.046 | 0.64 |
| 6_Y | 19_E | 1.045 | 0.64 |
| 82_L | 103_E | 1.043 | 0.63 |
| 49_R | 94_A | 1.039 | 0.63 |
| 87_L | 90_G | 1.039 | 0.63 |
| 85_Q | 119_V | 1.037 | 0.63 |
| 22_G | 34_F | 1.031 | 0.62 |
| 70_S | 81_A | 1.024 | 0.61 |
| 67_D | 126_G | 1.023 | 0.61 |
| 17_F | 21_T | 1.020 | 0.61 |
| 31_E | 35_V | 1.016 | 0.60 |
| 31_E | 34_F | 1.011 | 0.60 |
| 27_E | 31_E | 1.008 | 0.60 |
| 94_A | 112_E | 1.008 | 0.60 |
| 16_E | 21_T | 1.008 | 0.60 |
| 114_D | 122_L | 1.002 | 0.59 |
| 30_L | 36_F | 1.002 | 0.59 |
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 | 0.6769 | 99.2 | 0.525 | Contact Map |
| 4v1tA | 2 | 0.6077 | 81.4 | 0.832 | Contact Map |
| 3h5nA | 4 | 0.5769 | 79.6 | 0.835 | Contact Map |
| 4a0zA | 2 | 0.4 | 35.6 | 0.876 | Contact Map |
| 2gqqA | 4 | 0.4077 | 29.3 | 0.882 | Contact Map |
| 4un1A | 2 | 0.4 | 27 | 0.884 | Contact Map |
| 2cfxA | 8 | 0.3923 | 26 | 0.884 | Contact Map |
| 1i1gA | 2 | 0.3769 | 22.5 | 0.888 | Contact Map |
| 4pcqA | 4 | 0 | 21 | 0.89 | Contact Map |
| 3i4pA | 1 | 0.3769 | 20.9 | 0.89 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)