| r |
| ID: | 1508300248 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 142 (134) | ||
| Sequences: | 5918 (3952.6) | ||
| Seq/Len: | 44.164 | ||
| Nf(neff/√len): | 341.5 |
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: 44.164).
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 |
| 69_S | 73_Q | 3.762 | 1.00 |
| 118_D | 122_K | 2.943 | 1.00 |
| 70_G | 114_D | 2.904 | 1.00 |
| 113_K | 118_D | 2.567 | 1.00 |
| 119_E | 122_K | 2.347 | 1.00 |
| 19_V | 22_L | 2.339 | 1.00 |
| 116_P | 119_E | 2.307 | 1.00 |
| 117_Y | 137_L | 2.194 | 1.00 |
| 74_Y | 123_A | 2.087 | 1.00 |
| 69_S | 75_T | 2.082 | 1.00 |
| 29_L | 32_F | 2.049 | 1.00 |
| 68_V | 123_A | 1.889 | 1.00 |
| 121_I | 125_N | 1.842 | 1.00 |
| 82_R | 85_R | 1.772 | 1.00 |
| 18_I | 22_L | 1.749 | 1.00 |
| 117_Y | 120_I | 1.741 | 1.00 |
| 107_F | 127_L | 1.653 | 1.00 |
| 65_I | 110_G | 1.634 | 1.00 |
| 115_V | 119_E | 1.617 | 1.00 |
| 27_V | 31_I | 1.529 | 1.00 |
| 26_L | 31_I | 1.499 | 1.00 |
| 30_L | 34_A | 1.473 | 1.00 |
| 83_L | 122_K | 1.445 | 1.00 |
| 73_Q | 80_K | 1.439 | 1.00 |
| 126_L | 129_S | 1.430 | 1.00 |
| 67_E | 110_G | 1.399 | 0.99 |
| 125_N | 129_S | 1.385 | 0.99 |
| 108_L | 138_M | 1.359 | 0.99 |
| 66_V | 123_A | 1.344 | 0.99 |
| 70_G | 112_A | 1.340 | 0.99 |
| 45_V | 67_E | 1.320 | 0.99 |
| 22_L | 26_L | 1.302 | 0.99 |
| 66_V | 76_V | 1.301 | 0.99 |
| 19_V | 27_V | 1.300 | 0.99 |
| 64_V | 76_V | 1.291 | 0.99 |
| 25_L | 28_L | 1.283 | 0.99 |
| 68_V | 111_G | 1.281 | 0.99 |
| 124_L | 135_V | 1.257 | 0.99 |
| 22_L | 30_L | 1.232 | 0.98 |
| 72_G | 115_V | 1.219 | 0.98 |
| 111_G | 120_I | 1.215 | 0.98 |
| 102_N | 105_T | 1.189 | 0.98 |
| 107_F | 132_V | 1.186 | 0.98 |
| 22_L | 27_V | 1.185 | 0.98 |
| 97_S | 132_V | 1.168 | 0.97 |
| 111_G | 117_Y | 1.163 | 0.97 |
| 79_E | 91_V | 1.155 | 0.97 |
| 65_I | 108_L | 1.145 | 0.97 |
| 43_V | 121_I | 1.133 | 0.97 |
| 17_N | 27_V | 1.125 | 0.97 |
| 125_N | 128_H | 1.122 | 0.97 |
| 46_D | 113_K | 1.114 | 0.96 |
| 53_S | 139_T | 1.109 | 0.96 |
| 36_A | 39_I | 1.106 | 0.96 |
| 25_L | 32_F | 1.106 | 0.96 |
| 91_V | 94_E | 1.105 | 0.96 |
| 66_V | 127_L | 1.104 | 0.96 |
| 46_D | 114_D | 1.099 | 0.96 |
| 87_P | 126_L | 1.084 | 0.96 |
| 72_G | 119_E | 1.081 | 0.95 |
| 27_V | 34_A | 1.079 | 0.95 |
| 21_L | 27_V | 1.061 | 0.95 |
| 16_I | 27_V | 1.061 | 0.95 |
| 121_I | 139_T | 1.055 | 0.95 |
| 83_L | 119_E | 1.055 | 0.95 |
| 110_G | 138_M | 1.053 | 0.95 |
| 29_L | 33_M | 1.052 | 0.95 |
| 83_L | 126_L | 1.029 | 0.94 |
| 26_L | 32_F | 1.027 | 0.94 |
| 126_L | 130_A | 1.022 | 0.93 |
| 24_V | 27_V | 1.016 | 0.93 |
| 47_L | 117_Y | 1.013 | 0.93 |
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 | |
| 2pfuA | 1 | 0.669 | 99.4 | 0.488 | Contact Map |
| 2jwkA | 2 | 0.4859 | 98.7 | 0.617 | Contact Map |
| 2w3zA | 1 | 0.4648 | 40.3 | 0.877 | Contact Map |
| 3w5fA | 2 | 0.4155 | 8.9 | 0.91 | Contact Map |
| 3wu2K | 2 | 0.2606 | 6.6 | 0.916 | Contact Map |
| 1uuqA | 1 | 0.4577 | 4.7 | 0.921 | Contact Map |
| 3gycA | 2 | 0.3451 | 4.5 | 0.921 | Contact Map |
| 2d2rA | 2 | 0.2746 | 4.3 | 0.922 | Contact Map |
| 4q9mA | 2 | 0.2958 | 4 | 0.924 | Contact Map |
| 2jvfA | 1 | 0.5845 | 3.9 | 0.924 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)