| X1L |
| ID: | 1504171888 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 136 (123) | ||
| Sequences: | 162 (121.5) | ||
| Seq/Len: | 1.317 | ||
| Nf(neff/√len): | 11.0 |
HHblits Results: (2016_02)
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: 1.317).
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 |
| 108_E | 115_R | 2.965 | 1.00 |
| 109_A | 113_L | 2.109 | 0.98 |
| 52_S | 60_D | 1.598 | 0.88 |
| 108_E | 112_A | 1.577 | 0.87 |
| 48_L | 119_R | 1.573 | 0.87 |
| 38_L | 43_I | 1.498 | 0.83 |
| 38_L | 92_L | 1.491 | 0.83 |
| 51_T | 60_D | 1.484 | 0.83 |
| 51_T | 58_G | 1.469 | 0.82 |
| 110_H | 117_A | 1.460 | 0.81 |
| 87_D | 125_V | 1.432 | 0.79 |
| 64_A | 75_A | 1.408 | 0.78 |
| 85_D | 90_R | 1.383 | 0.76 |
| 84_P | 89_I | 1.295 | 0.69 |
| 87_D | 90_R | 1.294 | 0.69 |
| 19_E | 52_S | 1.291 | 0.69 |
| 51_T | 59_A | 1.284 | 0.68 |
| 7_L | 126_L | 1.255 | 0.65 |
| 3_D | 8_Q | 1.250 | 0.65 |
| 86_D | 96_R | 1.241 | 0.64 |
| 46_W | 116_I | 1.231 | 0.63 |
| 38_L | 80_W | 1.226 | 0.63 |
| 21_A | 81_A | 1.224 | 0.63 |
| 34_S | 46_W | 1.212 | 0.61 |
| 75_A | 119_R | 1.212 | 0.61 |
| 47_L | 76_A | 1.170 | 0.57 |
| 2_E | 11_K | 1.166 | 0.57 |
| 68_F | 120_Y | 1.163 | 0.57 |
| 119_R | 122_N | 1.158 | 0.56 |
| 70_E | 109_A | 1.157 | 0.56 |
| 90_R | 93_V | 1.155 | 0.56 |
| 76_A | 113_L | 1.154 | 0.56 |
| 7_L | 45_K | 1.152 | 0.56 |
| 107_E | 120_Y | 1.152 | 0.56 |
| 77_H | 109_A | 1.141 | 0.55 |
| 8_Q | 14_E | 1.129 | 0.53 |
| 75_A | 117_A | 1.113 | 0.52 |
| 69_V | 94_L | 1.104 | 0.51 |
| 39_W | 75_A | 1.103 | 0.51 |
| 44_R | 48_L | 1.095 | 0.50 |
| 108_E | 116_I | 1.089 | 0.49 |
| 105_E | 118_K | 1.088 | 0.49 |
| 38_L | 65_D | 1.088 | 0.49 |
| 31_I | 41_Q | 1.077 | 0.48 |
| 19_E | 60_D | 1.073 | 0.48 |
| 108_E | 123_A | 1.072 | 0.48 |
| 36_K | 45_K | 1.070 | 0.47 |
| 41_Q | 114_Y | 1.067 | 0.47 |
| 25_A | 77_H | 1.059 | 0.46 |
| 43_I | 76_A | 1.057 | 0.46 |
| 12_M | 41_Q | 1.054 | 0.46 |
| 58_G | 100_D | 1.047 | 0.45 |
| 17_E | 78_I | 1.047 | 0.45 |
| 54_T | 120_Y | 1.045 | 0.45 |
| 4_T | 70_E | 1.044 | 0.45 |
| 112_A | 116_I | 1.040 | 0.45 |
| 49_N | 106_D | 1.036 | 0.44 |
| 49_N | 70_E | 1.030 | 0.44 |
| 59_A | 123_A | 1.029 | 0.43 |
| 31_I | 99_M | 1.022 | 0.43 |
| 33_P | 71_D | 1.020 | 0.43 |
| 18_A | 31_I | 1.015 | 0.42 |
| 26_K | 117_A | 1.010 | 0.42 |
| 19_E | 101_E | 1.009 | 0.41 |
| 104_E | 122_N | 1.008 | 0.41 |
| 39_W | 64_A | 1.006 | 0.41 |
| 42_K | 50_S | 1.005 | 0.41 |
| 112_A | 125_V | 1.001 | 0.41 |
| 4_T | 39_W | 1.000 | 0.41 |
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 | |
| 3pieA | 4 | 0.875 | 98.7 | 0.71 | Contact Map |
| 1mszA | 1 | 0.4559 | 70 | 0.889 | Contact Map |
| 1whrA | 1 | 0.7794 | 19.6 | 0.921 | Contact Map |
| 1ug8A | 1 | 0.5662 | 12 | 0.928 | Contact Map |
| 1byyA | 1 | 0.1544 | 10.6 | 0.93 | Contact Map |
| 1vw4T | 1 | 0.3088 | 9.7 | 0.931 | Contact Map |
| 3eabG | 6 | 0.3088 | 9.2 | 0.931 | Contact Map |
| 1nkdA | 1 | 0.3676 | 8.9 | 0.932 | Contact Map |
| 4gfqA | 1 | 0.7206 | 7 | 0.935 | Contact Map |
| 2qt7A | 2 | 0.6397 | 7 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)