| test |
| ID: | 1451404942 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 87 (82) | ||
| Sequences: | 116 (113) | ||
| Seq/Len: | 1.415 | ||
| Nf(neff/√len): | 12.5 |
HHblits Results: (2015_06)
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: 1.415).
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 |
| 19_L | 69_V | 2.701 | 1.00 |
| 40_H | 44_I | 2.355 | 0.99 |
| 78_A | 83_G | 2.273 | 0.99 |
| 64_S | 67_G | 2.091 | 0.98 |
| 12_E | 73_K | 1.900 | 0.97 |
| 46_E | 81_K | 1.838 | 0.96 |
| 21_E | 33_V | 1.649 | 0.91 |
| 61_R | 71_E | 1.612 | 0.90 |
| 79_N | 83_G | 1.587 | 0.89 |
| 27_V | 37_L | 1.573 | 0.88 |
| 31_D | 38_L | 1.516 | 0.86 |
| 70_K | 74_E | 1.492 | 0.85 |
| 50_G | 53_L | 1.456 | 0.83 |
| 23_E | 68_I | 1.439 | 0.82 |
| 22_I | 30_T | 1.428 | 0.81 |
| 17_Q | 68_I | 1.409 | 0.80 |
| 17_Q | 20_K | 1.405 | 0.79 |
| 63_D | 67_G | 1.345 | 0.75 |
| 18_L | 41_F | 1.338 | 0.75 |
| 52_D | 56_Y | 1.335 | 0.74 |
| 42_V | 51_T | 1.320 | 0.73 |
| 37_L | 40_H | 1.314 | 0.73 |
| 49_D | 58_S | 1.309 | 0.72 |
| 16_V | 69_V | 1.213 | 0.64 |
| 19_L | 43_K | 1.196 | 0.62 |
| 45_T | 70_K | 1.192 | 0.62 |
| 40_H | 43_K | 1.183 | 0.61 |
| 37_L | 44_I | 1.138 | 0.56 |
| 6_S | 11_T | 1.075 | 0.50 |
| 57_P | 63_D | 1.056 | 0.48 |
| 41_F | 50_G | 1.050 | 0.48 |
| 51_T | 55_Y | 1.048 | 0.47 |
| 75_W | 84_F | 1.047 | 0.47 |
| 4_K | 14_E | 1.031 | 0.46 |
| 46_E | 76_R | 1.023 | 0.45 |
| 11_T | 14_E | 1.022 | 0.45 |
| 21_E | 37_L | 1.014 | 0.44 |
| 60_N | 68_I | 1.009 | 0.43 |
| 46_E | 79_N | 1.002 | 0.43 |
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 | |
| 1fr2A | 1 | 0.954 | 100 | 0.103 | Contact Map |
| 1unkA | 4 | 0.9885 | 100 | 0.104 | Contact Map |
| 1gxgA | 1 | 0.977 | 100 | 0.113 | Contact Map |
| 4f37A | 2 | 0.977 | 100 | 0.115 | Contact Map |
| 4uhpB | 4 | 0 | 100 | 0.117 | Contact Map |
| 3u43A | 1 | 0.9655 | 100 | 0.127 | Contact Map |
| 2k0dX | 1 | 0.977 | 100 | 0.138 | Contact Map |
| 4qkoA | 4 | 0 | 100 | 0.143 | Contact Map |
| 3or1A | 2 | 0.8851 | 20.7 | 0.921 | Contact Map |
| 4h3kB | 2 | 0.6207 | 15.9 | 0.925 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)