| tryout |
| ID: | 1433325976 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 83 (79) | ||
| Sequences: | 295 (163.9) | ||
| Seq/Len: | 3.734 | ||
| Nf(neff/√len): | 18.4 |
Jackhmmer Results: (2015_01_07)
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: 3.734).
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 |
| 57_Q | 61_T | 1.752 | 0.99 |
| 22_K | 26_Y | 1.750 | 0.99 |
| 16_A | 22_K | 1.726 | 0.99 |
| 8_N | 16_A | 1.587 | 0.98 |
| 19_E | 26_Y | 1.536 | 0.98 |
| 17_E | 30_L | 1.363 | 0.94 |
| 20_R | 34_Q | 1.278 | 0.91 |
| 30_L | 53_E | 1.276 | 0.91 |
| 16_A | 20_R | 1.272 | 0.91 |
| 44_C | 54_S | 1.247 | 0.90 |
| 35_N | 50_T | 1.234 | 0.89 |
| 47_E | 56_E | 1.233 | 0.89 |
| 6_I | 10_R | 1.222 | 0.89 |
| 6_I | 15_E | 1.221 | 0.89 |
| 24_A | 27_G | 1.214 | 0.88 |
| 18_E | 38_Q | 1.202 | 0.88 |
| 18_E | 28_L | 1.192 | 0.87 |
| 19_E | 28_L | 1.188 | 0.87 |
| 14_K | 64_R | 1.184 | 0.87 |
| 8_N | 12_R | 1.181 | 0.87 |
| 61_T | 69_K | 1.176 | 0.86 |
| 22_K | 28_L | 1.164 | 0.85 |
| 45_R | 48_M | 1.147 | 0.84 |
| 32_E | 39_N | 1.139 | 0.84 |
| 23_A | 41_L | 1.117 | 0.82 |
| 57_Q | 67_E | 1.113 | 0.82 |
| 16_A | 28_L | 1.112 | 0.82 |
| 19_E | 22_K | 1.108 | 0.81 |
| 20_R | 30_L | 1.101 | 0.81 |
| 17_E | 67_E | 1.100 | 0.81 |
| 42_D | 50_T | 1.094 | 0.80 |
| 27_G | 31_V | 1.092 | 0.80 |
| 47_E | 57_Q | 1.087 | 0.80 |
| 16_A | 19_E | 1.080 | 0.79 |
| 6_I | 9_L | 1.065 | 0.78 |
| 23_A | 59_K | 1.063 | 0.77 |
| 7_T | 10_R | 1.054 | 0.77 |
| 42_D | 52_T | 1.048 | 0.76 |
| 32_E | 40_Q | 1.048 | 0.76 |
| 60_Y | 65_E | 1.039 | 0.75 |
| 64_R | 72_M | 1.037 | 0.75 |
| 19_E | 24_A | 1.021 | 0.73 |
| 71_R | 75_S | 1.013 | 0.73 |
| 10_R | 15_E | 1.011 | 0.72 |
| 73_L | 77_S | 1.011 | 0.72 |
| 55_Y | 58_E | 1.008 | 0.72 |
| 27_G | 30_L | 1.008 | 0.72 |
| 18_E | 41_L | 1.005 | 0.72 |
| 53_E | 57_Q | 1.004 | 0.72 |
| 21_L | 31_V | 1.003 | 0.71 |
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 | |
| 4ll8A | 1 | 0 | 51.6 | 0.818 | Contact Map |
| 2dfsA | 2 | 1 | 47.5 | 0.823 | Contact Map |
| 2bnxA | 2 | 0.3012 | 35.8 | 0.835 | Contact Map |
| 4rsiA | 1 | 0.5904 | 26.2 | 0.846 | Contact Map |
| 1i84S | 2 | 0 | 20.1 | 0.854 | Contact Map |
| 3ojaB | 1 | 0.9277 | 18.8 | 0.856 | Contact Map |
| 3ghgA | 4 | 0.8675 | 17.8 | 0.857 | Contact Map |
| 3tnuA | 1 | 0.8434 | 15 | 0.862 | Contact Map |
| 3vkgA | 2 | 0.8795 | 14.9 | 0.862 | Contact Map |
| 2v66B | 4 | 0.7349 | 13.5 | 0.865 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)