| T0765 - R0046 |
| ID: | 1399401415 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 128 (121) | ||
| Sequences: | 625 (480.8) | ||
| Seq/Len: | 5.165 | ||
| Nf(neff/√len): | 43.7 |
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: 5.165).
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 |
| 83_S | 86_Q | 3.915 | 1.00 |
| 39_L | 94_L | 2.759 | 1.00 |
| 78_L | 109_D | 2.708 | 1.00 |
| 56_V | 79_I | 2.171 | 1.00 |
| 59_H | 94_L | 2.018 | 1.00 |
| 36_E | 68_K | 1.935 | 1.00 |
| 27_W | 122_D | 1.862 | 1.00 |
| 11_Q | 15_L | 1.838 | 1.00 |
| 115_A | 119_R | 1.814 | 1.00 |
| 36_E | 80_K | 1.792 | 1.00 |
| 36_E | 109_D | 1.752 | 1.00 |
| 28_L | 32_V | 1.737 | 1.00 |
| 34_Q | 112_S | 1.727 | 1.00 |
| 58_H | 62_A | 1.530 | 0.99 |
| 26_F | 120_L | 1.526 | 0.99 |
| 91_K | 95_G | 1.474 | 0.98 |
| 8_S | 11_Q | 1.429 | 0.98 |
| 40_A | 107_L | 1.413 | 0.98 |
| 16_L | 20_L | 1.363 | 0.97 |
| 7_P | 11_Q | 1.331 | 0.96 |
| 36_E | 78_L | 1.307 | 0.96 |
| 57_W | 61_D | 1.299 | 0.96 |
| 10_R | 13_S | 1.293 | 0.96 |
| 47_G | 50_M | 1.282 | 0.95 |
| 7_P | 14_W | 1.282 | 0.95 |
| 9_L | 13_S | 1.262 | 0.95 |
| 19_S | 23_G | 1.238 | 0.94 |
| 56_V | 97_A | 1.222 | 0.93 |
| 68_K | 78_L | 1.175 | 0.92 |
| 10_R | 14_W | 1.171 | 0.91 |
| 43_P | 126_R | 1.164 | 0.91 |
| 12_F | 87_G | 1.156 | 0.91 |
| 109_D | 113_P | 1.151 | 0.90 |
| 93_V | 97_A | 1.148 | 0.90 |
| 81_F | 84_T | 1.140 | 0.90 |
| 36_E | 112_S | 1.132 | 0.89 |
| 65_I | 81_F | 1.120 | 0.89 |
| 38_T | 65_I | 1.107 | 0.88 |
| 43_P | 50_M | 1.106 | 0.88 |
| 80_K | 105_A | 1.087 | 0.87 |
| 41_I | 98_L | 1.083 | 0.87 |
| 77_L | 94_L | 1.075 | 0.86 |
| 8_S | 126_R | 1.068 | 0.85 |
| 59_H | 97_A | 1.068 | 0.85 |
| 43_P | 47_G | 1.058 | 0.85 |
| 84_T | 115_A | 1.055 | 0.85 |
| 61_D | 64_G | 1.055 | 0.85 |
| 40_A | 108_E | 1.044 | 0.84 |
| 7_P | 10_R | 1.038 | 0.83 |
| 120_L | 123_A | 1.038 | 0.83 |
| 68_K | 82_D | 1.038 | 0.83 |
| 11_Q | 14_W | 1.035 | 0.83 |
| 26_F | 79_I | 1.030 | 0.83 |
| 51_P | 54_F | 1.018 | 0.82 |
| 41_I | 47_G | 1.013 | 0.81 |
| 60_L | 94_L | 1.012 | 0.81 |
| 64_G | 67_F | 1.007 | 0.81 |
| 37_A | 87_G | 1.003 | 0.80 |
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 | |
| 3aqpA | 2 | 0.9375 | 91.9 | 0.877 | Contact Map |
| 2gqcA | 1 | 0.5469 | 32.2 | 0.925 | Contact Map |
| 4m1bA | 2 | 0.6484 | 25.1 | 0.929 | Contact Map |
| 1jmtA | 1 | 0.6172 | 20.3 | 0.932 | Contact Map |
| 4a8xA | 1 | 0.6172 | 16.9 | 0.934 | Contact Map |
| 1xmxA | 1 | 0.7891 | 15.4 | 0.936 | Contact Map |
| 2x1fA | 1 | 0.6719 | 15 | 0.936 | Contact Map |
| 2lxiA | 1 | 0.6172 | 14.2 | 0.937 | Contact Map |
| 3p5tL | 6 | 0.5703 | 11.3 | 0.939 | Contact Map |
| 2ox0A | 2 | 0.8516 | 11.2 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)