| T0759 |
| ID: | 1398963037 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (106) | ||
| Sequences: | 181 (107.8) | ||
| Seq/Len: | 1.708 | ||
| Nf(neff/√len): | 10.5 |
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: 1.708).
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 |
| 14_I | 21_E | 1.794 | 0.96 |
| 9_S | 12_V | 1.680 | 0.94 |
| 97_S | 104_L | 1.600 | 0.92 |
| 69_G | 94_K | 1.481 | 0.88 |
| 18_P | 30_A | 1.467 | 0.87 |
| 11_M | 14_I | 1.449 | 0.86 |
| 15_H | 18_P | 1.399 | 0.83 |
| 45_E | 48_W | 1.392 | 0.83 |
| 22_L | 71_K | 1.383 | 0.82 |
| 17_D | 21_E | 1.374 | 0.82 |
| 22_L | 30_A | 1.364 | 0.81 |
| 74_I | 79_Q | 1.343 | 0.80 |
| 20_R | 31_G | 1.331 | 0.79 |
| 73_S | 78_L | 1.328 | 0.79 |
| 38_F | 108_Q | 1.314 | 0.78 |
| 10_H | 14_I | 1.309 | 0.77 |
| 71_K | 74_I | 1.308 | 0.77 |
| 23_S | 102_A | 1.306 | 0.77 |
| 84_T | 105_V | 1.282 | 0.75 |
| 14_I | 30_A | 1.261 | 0.74 |
| 26_E | 42_R | 1.253 | 0.73 |
| 7_H | 11_M | 1.246 | 0.72 |
| 74_I | 105_V | 1.221 | 0.70 |
| 13_V | 20_R | 1.213 | 0.69 |
| 12_V | 30_A | 1.203 | 0.68 |
| 29_R | 98_I | 1.189 | 0.67 |
| 53_V | 92_V | 1.188 | 0.67 |
| 13_V | 33_I | 1.173 | 0.66 |
| 87_H | 90_R | 1.167 | 0.65 |
| 21_E | 44_Q | 1.152 | 0.64 |
| 12_V | 32_L | 1.134 | 0.62 |
| 44_Q | 48_W | 1.133 | 0.62 |
| 9_S | 13_V | 1.130 | 0.61 |
| 34_D | 37_M | 1.116 | 0.60 |
| 52_S | 56_P | 1.111 | 0.59 |
| 76_E | 97_S | 1.102 | 0.59 |
| 71_K | 76_E | 1.100 | 0.58 |
| 83_L | 101_L | 1.099 | 0.58 |
| 14_I | 28_H | 1.096 | 0.58 |
| 99_Q | 103_V | 1.095 | 0.58 |
| 13_V | 24_P | 1.088 | 0.57 |
| 62_V | 66_R | 1.087 | 0.57 |
| 34_D | 76_E | 1.076 | 0.56 |
| 3_H | 7_H | 1.075 | 0.56 |
| 55_G | 104_L | 1.063 | 0.54 |
| 74_I | 97_S | 1.061 | 0.54 |
| 45_E | 52_S | 1.056 | 0.54 |
| 18_P | 25_E | 1.051 | 0.53 |
| 91_Y | 94_K | 1.051 | 0.53 |
| 25_E | 38_F | 1.046 | 0.53 |
| 62_V | 104_L | 1.041 | 0.52 |
| 49_E | 54_K | 1.040 | 0.52 |
| 8_H | 11_M | 1.038 | 0.52 |
| 62_V | 74_I | 1.031 | 0.51 |
| 9_S | 14_I | 1.026 | 0.50 |
| 8_H | 23_S | 1.025 | 0.50 |
| 18_P | 76_E | 1.021 | 0.50 |
| 3_H | 90_R | 1.019 | 0.50 |
| 20_R | 30_A | 1.018 | 0.50 |
| 51_I | 101_L | 1.017 | 0.49 |
| 94_K | 97_S | 1.007 | 0.48 |
| 10_H | 21_E | 1.006 | 0.48 |
| 78_L | 81_G | 1.006 | 0.48 |
| 76_E | 81_G | 1.002 | 0.48 |
| 12_V | 35_W | 1.002 | 0.48 |
| 8_H | 12_V | 1.001 | 0.48 |
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 | |
| 1lm5A | 2 | 0.8349 | 99.3 | 0.574 | Contact Map |
| 1lm7A | 2 | 0.8899 | 99.2 | 0.584 | Contact Map |
| 1pv8A | 2 | 0.3303 | 12.1 | 0.915 | Contact Map |
| 3iezA | 2 | 0.7982 | 6.8 | 0.924 | Contact Map |
| 1x0hA | 1 | 0.8716 | 5.2 | 0.928 | Contact Map |
| 4jwhA | 2 | 0.844 | 4.7 | 0.929 | Contact Map |
| 1h7nA | 1 | 0.4495 | 4.6 | 0.93 | Contact Map |
| 1nhaA | 1 | 0.2752 | 4.2 | 0.931 | Contact Map |
| 1v95A | 1 | 0.5505 | 4.1 | 0.931 | Contact Map |
| 1wh2A | 1 | 0.6697 | 3.9 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)