| Q8U3S5_PYRFU 1-150 1-110 |
| ID: | 1417480911 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 110 (97) | ||
| Sequences: | 1044 (779) | ||
| Seq/Len: | 10.763 | ||
| Nf(neff/√len): | 79.1 |
HHblits Results: (2013_03)
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: 10.763).
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 |
| 67_I | 74_W | 2.936 | 1.00 |
| 41_I | 79_K | 2.842 | 1.00 |
| 37_L | 41_I | 2.510 | 1.00 |
| 77_L | 82_A | 2.139 | 1.00 |
| 71_H | 75_A | 2.120 | 1.00 |
| 69_D | 104_P | 2.118 | 1.00 |
| 77_L | 80_L | 2.091 | 1.00 |
| 54_M | 85_A | 1.902 | 1.00 |
| 57_A | 66_L | 1.863 | 1.00 |
| 21_I | 87_S | 1.855 | 1.00 |
| 49_I | 86_P | 1.844 | 1.00 |
| 38_E | 42_E | 1.841 | 1.00 |
| 54_M | 87_S | 1.792 | 1.00 |
| 20_F | 84_R | 1.771 | 1.00 |
| 74_W | 78_Q | 1.743 | 1.00 |
| 26_M | 67_I | 1.664 | 1.00 |
| 22_E | 25_K | 1.571 | 1.00 |
| 20_F | 86_P | 1.557 | 1.00 |
| 99_V | 103_Y | 1.384 | 0.99 |
| 33_V | 36_E | 1.375 | 0.99 |
| 23_L | 74_W | 1.318 | 0.99 |
| 57_A | 94_D | 1.286 | 0.99 |
| 36_E | 72_H | 1.259 | 0.99 |
| 77_L | 85_A | 1.257 | 0.99 |
| 93_F | 96_G | 1.224 | 0.98 |
| 69_D | 72_H | 1.222 | 0.98 |
| 27_K | 64_E | 1.222 | 0.98 |
| 28_P | 67_I | 1.220 | 0.98 |
| 23_L | 26_M | 1.218 | 0.98 |
| 40_F | 76_G | 1.217 | 0.98 |
| 38_E | 79_K | 1.166 | 0.97 |
| 21_I | 65_Y | 1.165 | 0.97 |
| 97_V | 101_T | 1.156 | 0.97 |
| 43_S | 103_Y | 1.154 | 0.97 |
| 11_I | 14_K | 1.150 | 0.97 |
| 49_I | 77_L | 1.117 | 0.96 |
| 56_L | 87_S | 1.100 | 0.96 |
| 22_E | 26_M | 1.099 | 0.96 |
| 52_K | 104_P | 1.065 | 0.95 |
| 50_F | 106_F | 1.064 | 0.95 |
| 34_Q | 38_E | 1.061 | 0.95 |
| 41_I | 45_T | 1.060 | 0.95 |
| 32_L | 71_H | 1.054 | 0.95 |
| 101_T | 104_P | 1.050 | 0.94 |
| 102_W | 105_A | 1.049 | 0.94 |
| 37_L | 72_H | 1.033 | 0.94 |
| 41_I | 80_L | 1.025 | 0.93 |
| 44_V | 49_I | 1.009 | 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 | |
| 1vk1A | 1 | 0.8909 | 99.9 | 0.173 | Contact Map |
| 1vz0A | 8 | 0.8182 | 99.8 | 0.333 | Contact Map |
| 1yzsA | 1 | 0.9727 | 99.7 | 0.386 | Contact Map |
| 1xw3A | 1 | 0.9273 | 99.7 | 0.398 | Contact Map |
| 2hwjA | 6 | 0.8727 | 97.5 | 0.723 | Contact Map |
| 1r71A | 4 | 0.1545 | 92 | 0.809 | Contact Map |
| 2vg0A | 2 | 0.4727 | 21.2 | 0.894 | Contact Map |
| 1f75A | 2 | 0.4273 | 11 | 0.907 | Contact Map |
| 2d2rA | 2 | 0.4 | 10.4 | 0.908 | Contact Map |
| 3wqlA | 4 | 0.6182 | 10.2 | 0.908 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)