| BtS2R |
| ID: | 1516987032 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (171) | ||
| Sequences: | 398 (316.2) | ||
| Seq/Len: | 2.327 | ||
| Nf(neff/√len): | 24.2 |
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: 2.327).
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 |
| 22_I | 78_L | 2.267 | 1.00 |
| 50_Y | 54_F | 2.149 | 1.00 |
| 80_F | 99_P | 1.998 | 0.99 |
| 104_S | 158_L | 1.870 | 0.99 |
| 30_L | 74_L | 1.868 | 0.99 |
| 72_C | 106_H | 1.863 | 0.99 |
| 21_H | 81_F | 1.753 | 0.98 |
| 77_Q | 81_F | 1.737 | 0.98 |
| 55_K | 139_E | 1.707 | 0.97 |
| 157_L | 160_F | 1.690 | 0.97 |
| 111_L | 114_I | 1.647 | 0.96 |
| 170_E | 174_K | 1.636 | 0.96 |
| 22_I | 82_P | 1.602 | 0.96 |
| 14_L | 160_F | 1.588 | 0.95 |
| 17_Y | 21_H | 1.558 | 0.95 |
| 15_G | 85_A | 1.518 | 0.94 |
| 30_L | 110_T | 1.517 | 0.94 |
| 160_F | 164_N | 1.512 | 0.93 |
| 31_Q | 40_P | 1.502 | 0.93 |
| 25_T | 78_L | 1.492 | 0.93 |
| 19_L | 85_A | 1.463 | 0.92 |
| 73_E | 77_Q | 1.460 | 0.92 |
| 26_L | 78_L | 1.450 | 0.91 |
| 31_Q | 34_L | 1.447 | 0.91 |
| 143_L | 147_Y | 1.412 | 0.90 |
| 19_L | 22_I | 1.407 | 0.90 |
| 18_F | 103_Y | 1.385 | 0.89 |
| 86_Y | 90_K | 1.385 | 0.89 |
| 108_M | 154_P | 1.382 | 0.89 |
| 21_H | 25_T | 1.368 | 0.88 |
| 101_I | 156_I | 1.359 | 0.88 |
| 166_Y | 170_E | 1.338 | 0.86 |
| 11_E | 160_F | 1.337 | 0.86 |
| 8_R | 12_W | 1.334 | 0.86 |
| 32_G | 158_L | 1.311 | 0.85 |
| 81_F | 154_P | 1.307 | 0.85 |
| 25_T | 81_F | 1.305 | 0.84 |
| 71_F | 75_V | 1.295 | 0.84 |
| 88_F | 95_W | 1.294 | 0.84 |
| 50_Y | 56_D | 1.292 | 0.84 |
| 58_L | 109_T | 1.289 | 0.83 |
| 83_I | 153_I | 1.281 | 0.83 |
| 7_R | 12_W | 1.260 | 0.82 |
| 10_L | 13_F | 1.233 | 0.80 |
| 108_M | 115_L | 1.209 | 0.78 |
| 71_F | 156_I | 1.197 | 0.77 |
| 108_M | 158_L | 1.191 | 0.76 |
| 29_D | 35_P | 1.190 | 0.76 |
| 77_Q | 154_P | 1.182 | 0.75 |
| 5_G | 9_G | 1.178 | 0.75 |
| 46_L | 49_W | 1.176 | 0.75 |
| 57_P | 154_P | 1.175 | 0.75 |
| 74_L | 108_M | 1.173 | 0.75 |
| 21_H | 24_I | 1.162 | 0.74 |
| 128_H | 132_Q | 1.154 | 0.73 |
| 49_W | 52_E | 1.144 | 0.72 |
| 143_L | 150_Y | 1.140 | 0.72 |
| 98_T | 162_V | 1.140 | 0.72 |
| 77_Q | 147_Y | 1.139 | 0.72 |
| 65_W | 115_L | 1.136 | 0.71 |
| 133_G | 136_T | 1.135 | 0.71 |
| 98_T | 159_L | 1.128 | 0.71 |
| 74_L | 159_L | 1.118 | 0.70 |
| 32_G | 47_Q | 1.112 | 0.69 |
| 46_L | 52_E | 1.111 | 0.69 |
| 58_L | 66_F | 1.109 | 0.69 |
| 33_V | 70_L | 1.104 | 0.68 |
| 80_F | 84_A | 1.099 | 0.68 |
| 106_H | 113_P | 1.086 | 0.66 |
| 8_R | 11_E | 1.082 | 0.66 |
| 2_G | 5_G | 1.082 | 0.66 |
| 14_L | 157_L | 1.082 | 0.66 |
| 17_Y | 81_F | 1.081 | 0.66 |
| 100_A | 165_P | 1.081 | 0.66 |
| 40_P | 119_L | 1.080 | 0.66 |
| 49_W | 53_E | 1.077 | 0.65 |
| 50_Y | 73_E | 1.076 | 0.65 |
| 32_G | 59_L | 1.075 | 0.65 |
| 8_R | 18_F | 1.062 | 0.64 |
| 100_A | 104_S | 1.049 | 0.62 |
| 106_H | 109_T | 1.039 | 0.61 |
| 57_P | 121_D | 1.030 | 0.60 |
| 77_Q | 103_Y | 1.030 | 0.60 |
| 114_I | 164_N | 1.029 | 0.60 |
| 69_F | 113_P | 1.017 | 0.59 |
| 23_P | 110_T | 1.009 | 0.58 |
| 48_Q | 152_L | 1.008 | 0.58 |
| 84_A | 96_I | 1.003 | 0.57 |
| 96_I | 100_A | 1.001 | 0.57 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2ka4B | 1 | 0.2557 | 1.4 | 0.965 | Contact Map |
| 2qjyA | 6 | 0.3864 | 1.4 | 0.965 | Contact Map |
| 2mc7A | 1 | 0.1705 | 1.4 | 0.965 | Contact Map |
| 2mheA | 2 | 0.1761 | 1.3 | 0.966 | Contact Map |
| 3effK | 4 | 0.5568 | 1 | 0.968 | Contact Map |
| 1hznA | 1 | 0.1648 | 1 | 0.968 | Contact Map |
| 2wscI | 1 | 0.1364 | 0.9 | 0.97 | Contact Map |
| 3pblA | 2 | 0.8636 | 0.8 | 0.97 | Contact Map |
| 1b3tA | 2 | 0.3295 | 0.8 | 0.971 | Contact Map |
| 4ksnA | 4 | 0.1364 | 0.8 | 0.971 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)