| tspo-pfam |
| ID: | 1516638099 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 169 (155) | ||
| Sequences: | 2902 (2240.4) | ||
| Seq/Len: | 18.723 | ||
| Nf(neff/√len): | 180.0 |
Jackhmmer Results: (2016_04)
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: 18.723).
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 |
| 116_S | 145_A | 3.933 | 1.00 |
| 98_I | 111_D | 3.473 | 1.00 |
| 119_A | 144_L | 3.146 | 1.00 |
| 66_I | 130_S | 3.108 | 1.00 |
| 42_W | 149_V | 2.904 | 1.00 |
| 47_W | 51_P | 2.783 | 1.00 |
| 106_G | 155_W | 2.654 | 1.00 |
| 109_L | 152_Y | 2.355 | 1.00 |
| 91_L | 118_V | 2.321 | 1.00 |
| 16_S | 58_S | 2.254 | 1.00 |
| 18_G | 93_W | 2.105 | 1.00 |
| 122_T | 137_L | 2.000 | 1.00 |
| 123_T | 134_A | 1.958 | 1.00 |
| 127_H | 134_A | 1.878 | 1.00 |
| 84_L | 125_A | 1.858 | 1.00 |
| 135_R | 138_Y | 1.775 | 1.00 |
| 63_G | 137_L | 1.769 | 1.00 |
| 109_L | 151_N | 1.738 | 1.00 |
| 152_Y | 156_R | 1.726 | 1.00 |
| 153_Y | 156_R | 1.682 | 1.00 |
| 153_Y | 157_D | 1.673 | 1.00 |
| 116_S | 148_T | 1.648 | 1.00 |
| 33_W | 105_M | 1.584 | 1.00 |
| 122_T | 126_W | 1.558 | 1.00 |
| 116_S | 144_L | 1.540 | 1.00 |
| 112_L | 148_T | 1.507 | 1.00 |
| 39_K | 43_H | 1.493 | 1.00 |
| 71_L | 78_A | 1.478 | 1.00 |
| 98_I | 108_A | 1.477 | 1.00 |
| 57_Y | 92_N | 1.431 | 1.00 |
| 127_H | 135_R | 1.426 | 1.00 |
| 84_L | 121_A | 1.425 | 1.00 |
| 8_A | 65_Y | 1.407 | 0.99 |
| 38_Q | 157_D | 1.403 | 0.99 |
| 33_W | 103_R | 1.403 | 0.99 |
| 42_W | 153_Y | 1.370 | 0.99 |
| 15_P | 85_Y | 1.351 | 0.99 |
| 64_S | 82_L | 1.341 | 0.99 |
| 16_S | 19_G | 1.338 | 0.99 |
| 11_L | 64_S | 1.334 | 0.99 |
| 67_V | 126_W | 1.318 | 0.99 |
| 149_V | 153_Y | 1.286 | 0.99 |
| 112_L | 151_N | 1.286 | 0.99 |
| 34_Y | 43_H | 1.283 | 0.99 |
| 108_A | 111_D | 1.282 | 0.99 |
| 121_A | 125_A | 1.279 | 0.99 |
| 70_E | 130_S | 1.277 | 0.99 |
| 15_P | 61_G | 1.257 | 0.99 |
| 123_T | 141_L | 1.244 | 0.98 |
| 64_S | 85_Y | 1.238 | 0.98 |
| 39_K | 154_V | 1.188 | 0.98 |
| 123_T | 137_L | 1.176 | 0.98 |
| 63_G | 133_A | 1.151 | 0.97 |
| 90_A | 94_A | 1.148 | 0.97 |
| 91_L | 111_D | 1.093 | 0.96 |
| 80_V | 125_A | 1.092 | 0.96 |
| 81_P | 126_W | 1.090 | 0.96 |
| 109_L | 148_T | 1.083 | 0.96 |
| 127_H | 131_P | 1.064 | 0.95 |
| 94_A | 111_D | 1.062 | 0.95 |
| 116_S | 119_A | 1.057 | 0.95 |
| 11_L | 15_P | 1.044 | 0.94 |
| 41_S | 153_Y | 1.039 | 0.94 |
| 104_Q | 107_W | 1.030 | 0.94 |
| 116_S | 141_L | 1.022 | 0.93 |
| 63_G | 122_T | 1.022 | 0.93 |
| 10_G | 14_V | 1.019 | 0.93 |
| 65_Y | 69_K | 1.017 | 0.93 |
| 120_T | 141_L | 1.016 | 0.93 |
| 67_V | 81_P | 1.009 | 0.93 |
| 54_G | 58_S | 1.009 | 0.93 |
| 142_A | 146_F | 1.008 | 0.93 |
| 30_G | 46_R | 1.001 | 0.92 |
| 60_M | 64_S | 1.001 | 0.92 |
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 | |
| 2mgyA | 1 | 1 | 100 | 0.165 | Contact Map |
| 4uc1A | 3 | 0.929 | 100 | 0.226 | Contact Map |
| 4ryoA | 1 | 0 | 100 | 0.242 | Contact Map |
| 1yewC | 3 | 0.5207 | 6.6 | 0.948 | Contact Map |
| 4phzK | 3 | 0.7101 | 5.2 | 0.951 | Contact Map |
| 2a65A | 1 | 0.432 | 4.7 | 0.952 | Contact Map |
| 3w4tA | 1 | 0.7515 | 4.4 | 0.953 | Contact Map |
| 4xp4A | 1 | 0 | 4.1 | 0.953 | Contact Map |
| 3zuxA | 1 | 0.8462 | 1.9 | 0.96 | Contact Map |
| 3orgA | 4 | 0.426 | 1.9 | 0.96 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)