| T0855 |
| ID: | 1405537039 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 119 (108) | ||
| Sequences: | 362 (326.1) | ||
| Seq/Len: | 3.352 | ||
| Nf(neff/√len): | 31.4 |
Jackhmmer Results: (2014_04_16)
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: 3.352).
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 |
| 75_I | 92_L | 2.034 | 1.00 |
| 101_Q | 104_S | 1.710 | 0.99 |
| 35_G | 63_I | 1.638 | 0.98 |
| 73_V | 94_Q | 1.535 | 0.97 |
| 77_Y | 100_Y | 1.524 | 0.97 |
| 12_V | 16_L | 1.497 | 0.96 |
| 77_Y | 90_L | 1.497 | 0.96 |
| 71_Q | 96_K | 1.483 | 0.96 |
| 79_S | 83_T | 1.467 | 0.96 |
| 108_E | 111_D | 1.442 | 0.95 |
| 81_R | 85_L | 1.441 | 0.95 |
| 82_N | 96_K | 1.427 | 0.95 |
| 40_S | 65_F | 1.423 | 0.95 |
| 79_S | 85_L | 1.419 | 0.95 |
| 76_K | 89_A | 1.413 | 0.95 |
| 107_R | 110_D | 1.380 | 0.94 |
| 29_A | 39_P | 1.370 | 0.93 |
| 71_Q | 75_I | 1.358 | 0.93 |
| 104_S | 114_A | 1.346 | 0.93 |
| 11_G | 15_G | 1.278 | 0.90 |
| 36_I | 49_D | 1.269 | 0.89 |
| 31_Q | 34_Y | 1.268 | 0.89 |
| 22_W | 35_G | 1.256 | 0.89 |
| 32_L | 35_G | 1.250 | 0.88 |
| 56_A | 59_Q | 1.246 | 0.88 |
| 87_A | 107_R | 1.238 | 0.88 |
| 84_K | 88_K | 1.233 | 0.88 |
| 34_Y | 40_S | 1.226 | 0.87 |
| 94_Q | 114_A | 1.225 | 0.87 |
| 65_F | 115_G | 1.215 | 0.86 |
| 29_A | 35_G | 1.190 | 0.85 |
| 12_V | 15_G | 1.188 | 0.85 |
| 11_G | 14_A | 1.179 | 0.84 |
| 109_V | 113_V | 1.172 | 0.84 |
| 53_L | 56_A | 1.168 | 0.83 |
| 90_L | 101_Q | 1.168 | 0.83 |
| 9_Q | 12_V | 1.165 | 0.83 |
| 101_Q | 107_R | 1.160 | 0.83 |
| 40_S | 47_V | 1.152 | 0.82 |
| 108_E | 114_A | 1.133 | 0.81 |
| 37_V | 42_T | 1.131 | 0.81 |
| 90_L | 107_R | 1.125 | 0.80 |
| 102_T | 107_R | 1.121 | 0.80 |
| 95_L | 98_E | 1.117 | 0.79 |
| 10_I | 15_G | 1.116 | 0.79 |
| 88_K | 109_V | 1.110 | 0.79 |
| 17_A | 21_E | 1.083 | 0.76 |
| 76_K | 96_K | 1.059 | 0.74 |
| 12_V | 17_A | 1.056 | 0.74 |
| 30_N | 48_D | 1.055 | 0.74 |
| 47_V | 59_Q | 1.054 | 0.74 |
| 62_T | 80_Q | 1.053 | 0.74 |
| 10_I | 14_A | 1.049 | 0.73 |
| 54_V | 58_D | 1.043 | 0.73 |
| 84_K | 89_A | 1.039 | 0.72 |
| 80_Q | 84_K | 1.034 | 0.72 |
| 27_I | 113_V | 1.026 | 0.71 |
| 13_L | 16_L | 1.024 | 0.71 |
| 108_E | 113_V | 1.021 | 0.70 |
| 80_Q | 115_G | 1.013 | 0.69 |
| 17_A | 22_W | 1.005 | 0.69 |
| 107_R | 114_A | 1.003 | 0.68 |
| 14_A | 18_I | 1.001 | 0.68 |
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 | |
| 2kvzA | 1 | 0.437 | 99.1 | 0.438 | Contact Map |
| 2kt7A | 1 | 0.4034 | 98.8 | 0.513 | Contact Map |
| 3i57A | 2 | 0.4118 | 96.5 | 0.698 | Contact Map |
| 2kywA | 1 | 0.4034 | 91.4 | 0.765 | Contact Map |
| 4m00A | 1 | 0.9496 | 87.8 | 0.781 | Contact Map |
| 3lyyA | 2 | 0.5798 | 70.3 | 0.817 | Contact Map |
| 2lfiA | 1 | 0.7059 | 70.1 | 0.817 | Contact Map |
| 3nz3A | 1 | 0.5294 | 57.2 | 0.831 | Contact Map |
| 2x5pA | 1 | 0.4706 | 12 | 0.881 | Contact Map |
| 3e8vA | 1 | 0.4118 | 10 | 0.885 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)