| odoratant |
| ID: | 1506564757 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (141) | ||
| Sequences: | 3113 (1969.2) | ||
| Seq/Len: | 22.078 | ||
| Nf(neff/√len): | 165.8 |
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: 22.078).
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 |
| 30_T | 37_N | 3.138 | 1.00 |
| 80_K | 83_E | 3.130 | 1.00 |
| 22_F | 42_T | 2.859 | 1.00 |
| 115_K | 134_D | 2.853 | 1.00 |
| 2_H | 28_N | 2.620 | 1.00 |
| 32_E | 35_N | 2.569 | 1.00 |
| 63_Q | 75_Y | 2.544 | 1.00 |
| 121_D | 125_R | 2.440 | 1.00 |
| 5_T | 8_L | 2.338 | 1.00 |
| 120_E | 124_N | 2.335 | 1.00 |
| 37_N | 52_Y | 2.140 | 1.00 |
| 35_N | 56_F | 2.037 | 1.00 |
| 128_R | 131_N | 1.971 | 1.00 |
| 6_V | 105_G | 1.950 | 1.00 |
| 88_I | 127_F | 1.947 | 1.00 |
| 112_N | 116_K | 1.934 | 1.00 |
| 2_H | 26_I | 1.900 | 1.00 |
| 103_L | 118_F | 1.860 | 1.00 |
| 78_S | 84_Y | 1.857 | 1.00 |
| 121_D | 124_N | 1.838 | 1.00 |
| 101_A | 132_I | 1.783 | 1.00 |
| 78_S | 121_D | 1.732 | 1.00 |
| 114_I | 117_R | 1.731 | 1.00 |
| 86_K | 118_F | 1.716 | 1.00 |
| 27_Q | 40_F | 1.697 | 1.00 |
| 84_Y | 114_I | 1.689 | 1.00 |
| 116_K | 120_E | 1.682 | 1.00 |
| 105_G | 110_L | 1.677 | 1.00 |
| 115_K | 119_E | 1.669 | 1.00 |
| 101_A | 122_F | 1.633 | 1.00 |
| 35_N | 54_T | 1.556 | 1.00 |
| 111_S | 114_I | 1.547 | 1.00 |
| 119_E | 129_R | 1.541 | 1.00 |
| 28_N | 41_L | 1.453 | 1.00 |
| 118_F | 121_D | 1.421 | 1.00 |
| 41_L | 48_C | 1.414 | 1.00 |
| 86_K | 121_D | 1.406 | 0.99 |
| 30_T | 39_F | 1.382 | 0.99 |
| 78_S | 117_R | 1.356 | 0.99 |
| 103_L | 110_L | 1.326 | 0.99 |
| 74_V | 87_F | 1.300 | 0.99 |
| 79_S | 85_A | 1.263 | 0.99 |
| 123_M | 129_R | 1.261 | 0.99 |
| 6_V | 110_L | 1.226 | 0.98 |
| 32_E | 37_N | 1.204 | 0.98 |
| 78_S | 86_K | 1.185 | 0.98 |
| 4_H | 137_E | 1.182 | 0.98 |
| 57_K | 61_A | 1.161 | 0.97 |
| 129_R | 132_I | 1.155 | 0.97 |
| 117_R | 121_D | 1.151 | 0.97 |
| 78_S | 118_F | 1.146 | 0.97 |
| 23_R | 136_S | 1.138 | 0.97 |
| 4_H | 108_P | 1.134 | 0.97 |
| 39_F | 52_Y | 1.134 | 0.97 |
| 76_Y | 79_S | 1.131 | 0.97 |
| 86_K | 110_L | 1.104 | 0.96 |
| 8_L | 25_F | 1.102 | 0.96 |
| 86_K | 122_F | 1.098 | 0.96 |
| 43_R | 46_G | 1.065 | 0.95 |
| 56_F | 71_T | 1.036 | 0.94 |
| 112_N | 115_K | 1.025 | 0.93 |
| 41_L | 50_P | 1.020 | 0.93 |
| 56_F | 65_K | 1.018 | 0.93 |
| 82_N | 85_A | 1.016 | 0.93 |
| 120_E | 123_M | 1.008 | 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 | |
| 2ra6A | 4 | 1 | 99.9 | 0.07 | Contact Map |
| 1e5pA | 4 | 0.9929 | 99.9 | 0.073 | Contact Map |
| 3l4rA | 1 | 1 | 99.9 | 0.082 | Contact Map |
| 1ew3A | 1 | 1 | 99.9 | 0.085 | Contact Map |
| 1dzkA | 2 | 0.9858 | 99.9 | 0.085 | Contact Map |
| 2a2uA | 4 | 1 | 99.9 | 0.088 | Contact Map |
| 2hlvA | 1 | 0.9858 | 99.9 | 0.092 | Contact Map |
| 3kffA | 1 | 1 | 99.9 | 0.095 | Contact Map |
| 3saoA | 2 | 1 | 99.9 | 0.098 | Contact Map |
| 4r0bA | 1 | 1 | 99.9 | 0.098 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)