| D |
| ID: | 1508859409 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (129) | ||
| Sequences: | 4951 (3321.7) | ||
| Seq/Len: | 38.380 | ||
| Nf(neff/√len): | 292.5 |
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: 38.380).
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_K | 73_S | 3.613 | 1.00 |
| 70_A | 109_T | 2.669 | 1.00 |
| 113_E | 117_K | 2.656 | 1.00 |
| 108_K | 113_E | 2.573 | 1.00 |
| 73_S | 80_P | 2.390 | 1.00 |
| 112_Y | 132_L | 2.274 | 1.00 |
| 87_I | 124_Q | 2.167 | 1.00 |
| 82_T | 85_T | 2.161 | 1.00 |
| 79_D | 89_A | 2.155 | 1.00 |
| 21_T | 24_I | 2.145 | 1.00 |
| 114_T | 117_K | 2.024 | 1.00 |
| 68_V | 118_V | 2.011 | 1.00 |
| 74_M | 118_V | 1.975 | 1.00 |
| 111_D | 114_T | 1.956 | 1.00 |
| 31_L | 34_F | 1.927 | 1.00 |
| 112_Y | 115_L | 1.829 | 1.00 |
| 69_K | 75_F | 1.799 | 1.00 |
| 94_T | 127_Y | 1.696 | 1.00 |
| 20_V | 24_I | 1.638 | 1.00 |
| 85_T | 89_A | 1.610 | 1.00 |
| 116_M | 120_D | 1.587 | 1.00 |
| 75_F | 80_P | 1.516 | 1.00 |
| 90_L | 122_L | 1.507 | 1.00 |
| 83_D | 117_K | 1.459 | 1.00 |
| 67_S | 105_R | 1.409 | 1.00 |
| 47_V | 67_S | 1.377 | 0.99 |
| 29_V | 33_I | 1.369 | 0.99 |
| 65_Y | 105_R | 1.364 | 0.99 |
| 110_V | 114_T | 1.346 | 0.99 |
| 102_I | 122_L | 1.323 | 0.99 |
| 87_I | 91_N | 1.321 | 0.99 |
| 21_T | 25_D | 1.310 | 0.99 |
| 106_A | 115_L | 1.305 | 0.99 |
| 87_I | 121_T | 1.292 | 0.99 |
| 121_T | 124_Q | 1.259 | 0.99 |
| 28_L | 33_I | 1.251 | 0.99 |
| 31_L | 35_M | 1.217 | 0.98 |
| 103_F | 133_V | 1.216 | 0.98 |
| 64_V | 76_I | 1.209 | 0.98 |
| 66_L | 76_I | 1.207 | 0.98 |
| 87_I | 125_A | 1.207 | 0.98 |
| 72_N | 110_V | 1.202 | 0.98 |
| 67_S | 75_F | 1.196 | 0.98 |
| 32_I | 36_V | 1.193 | 0.98 |
| 70_A | 107_D | 1.188 | 0.98 |
| 120_D | 124_Q | 1.180 | 0.98 |
| 55_T | 134_G | 1.176 | 0.98 |
| 106_A | 112_Y | 1.175 | 0.98 |
| 53_T | 124_Q | 1.156 | 0.97 |
| 76_I | 89_A | 1.153 | 0.97 |
| 19_N | 29_V | 1.130 | 0.97 |
| 89_A | 92_A | 1.129 | 0.97 |
| 72_N | 114_T | 1.109 | 0.96 |
| 91_N | 95_E | 1.108 | 0.96 |
| 102_I | 127_Y | 1.107 | 0.96 |
| 119_M | 130_I | 1.097 | 0.96 |
| 52_S | 134_G | 1.087 | 0.96 |
| 97_K | 100_T | 1.087 | 0.96 |
| 21_T | 29_V | 1.076 | 0.95 |
| 49_L | 112_Y | 1.073 | 0.95 |
| 18_I | 29_V | 1.058 | 0.95 |
| 24_I | 32_I | 1.052 | 0.95 |
| 18_I | 25_D | 1.049 | 0.94 |
| 83_D | 121_T | 1.039 | 0.94 |
| 65_Y | 103_F | 1.037 | 0.94 |
| 88_T | 91_N | 1.021 | 0.93 |
| 24_I | 28_L | 1.014 | 0.93 |
| 19_N | 33_I | 1.013 | 0.93 |
| 29_V | 39_P | 1.011 | 0.93 |
| 68_V | 106_A | 1.007 | 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 | 0.7021 | 99.7 | 0.49 | Contact Map |
| 2jwkA | 2 | 0.4894 | 99.1 | 0.633 | Contact Map |
| 2w3zA | 1 | 0.5319 | 74.7 | 0.874 | Contact Map |
| 3ghfA | 1 | 0.5603 | 33.2 | 0.903 | Contact Map |
| 1hf2A | 4 | 0.5603 | 21.5 | 0.912 | Contact Map |
| 1uuqA | 1 | 0.4894 | 14.9 | 0.918 | Contact Map |
| 3l07A | 2 | 0.5106 | 14 | 0.918 | Contact Map |
| 3w5fA | 2 | 0.4468 | 11.6 | 0.921 | Contact Map |
| 4a26A | 2 | 0.4894 | 9 | 0.925 | Contact Map |
| 4madA | 2 | 0.4255 | 8.7 | 0.926 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)