| JHBP |
| ID: | 1398154428 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 227 (210) | ||
| Sequences: | 561 (452.9) | ||
| Seq/Len: | 2.671 | ||
| Nf(neff/√len): | 31.3 |
HHblits Results: (2013_03)
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: 2.671).
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 |
| 165_S | 169_S | 2.740 | 1.00 |
| 43_D | 73_K | 2.652 | 1.00 |
| 96_D | 113_S | 2.534 | 1.00 |
| 121_D | 151_F | 2.494 | 1.00 |
| 140_G | 143_H | 2.418 | 1.00 |
| 11_C | 18_C | 2.324 | 1.00 |
| 34_I | 37_Y | 2.258 | 1.00 |
| 8_L | 22_A | 2.068 | 1.00 |
| 66_N | 96_D | 1.950 | 0.99 |
| 110_Q | 163_L | 1.915 | 0.99 |
| 27_L | 75_Q | 1.870 | 0.99 |
| 98_H | 111_S | 1.830 | 0.99 |
| 46_V | 68_N | 1.723 | 0.98 |
| 24_E | 27_L | 1.689 | 0.98 |
| 147_Q | 189_T | 1.662 | 0.97 |
| 97_L | 104_V | 1.607 | 0.97 |
| 97_L | 112_K | 1.596 | 0.97 |
| 53_I | 61_V | 1.557 | 0.96 |
| 138_D | 143_H | 1.553 | 0.96 |
| 101_G | 107_L | 1.532 | 0.95 |
| 107_L | 176_G | 1.482 | 0.94 |
| 83_D | 86_A | 1.458 | 0.93 |
| 173_K | 179_S | 1.456 | 0.93 |
| 157_G | 161_I | 1.446 | 0.93 |
| 195_I | 199_A | 1.414 | 0.92 |
| 158_E | 183_D | 1.401 | 0.92 |
| 161_I | 167_L | 1.396 | 0.91 |
| 40_W | 205_S | 1.373 | 0.90 |
| 67_L | 114_F | 1.333 | 0.89 |
| 185_E | 189_T | 1.326 | 0.88 |
| 192_Q | 196_C | 1.320 | 0.88 |
| 10_P | 218_P | 1.306 | 0.87 |
| 159_P | 163_L | 1.302 | 0.87 |
| 60_I | 103_I | 1.280 | 0.86 |
| 103_I | 110_Q | 1.277 | 0.86 |
| 213_S | 217_L | 1.274 | 0.85 |
| 22_A | 26_F | 1.264 | 0.85 |
| 7_L | 22_A | 1.264 | 0.85 |
| 75_Q | 181_E | 1.263 | 0.85 |
| 177_N | 181_E | 1.255 | 0.84 |
| 30_T | 43_D | 1.254 | 0.84 |
| 39_I | 50_L | 1.246 | 0.84 |
| 164_S | 168_S | 1.245 | 0.84 |
| 72_L | 116_G | 1.243 | 0.84 |
| 205_S | 213_S | 1.221 | 0.82 |
| 212_A | 216_I | 1.211 | 0.81 |
| 188_K | 207_V | 1.207 | 0.81 |
| 79_D | 177_N | 1.198 | 0.80 |
| 139_N | 143_H | 1.194 | 0.80 |
| 108_T | 178_N | 1.184 | 0.79 |
| 110_Q | 162_T | 1.182 | 0.79 |
| 101_G | 181_E | 1.173 | 0.78 |
| 107_L | 184_M | 1.170 | 0.78 |
| 69_I | 72_L | 1.154 | 0.77 |
| 10_P | 13_L | 1.149 | 0.76 |
| 31_S | 73_K | 1.147 | 0.76 |
| 16_M | 19_L | 1.139 | 0.75 |
| 192_Q | 204_I | 1.136 | 0.75 |
| 161_I | 180_L | 1.135 | 0.75 |
| 75_Q | 208_H | 1.134 | 0.75 |
| 89_V | 210_I | 1.124 | 0.74 |
| 110_Q | 180_L | 1.120 | 0.74 |
| 159_P | 168_S | 1.119 | 0.74 |
| 168_S | 172_E | 1.108 | 0.73 |
| 69_I | 114_F | 1.098 | 0.72 |
| 92_K | 217_L | 1.084 | 0.70 |
| 196_C | 199_A | 1.082 | 0.70 |
| 200_E | 205_S | 1.078 | 0.70 |
| 160_K | 164_S | 1.076 | 0.69 |
| 97_L | 107_L | 1.076 | 0.69 |
| 33_G | 188_K | 1.074 | 0.69 |
| 34_I | 94_K | 1.074 | 0.69 |
| 166_D | 181_E | 1.071 | 0.69 |
| 171_L | 180_L | 1.071 | 0.69 |
| 51_D | 66_N | 1.069 | 0.69 |
| 38_D | 149_E | 1.069 | 0.69 |
| 34_I | 43_D | 1.068 | 0.69 |
| 104_V | 191_R | 1.059 | 0.68 |
| 115_T | 119_T | 1.050 | 0.67 |
| 23_T | 27_L | 1.042 | 0.66 |
| 31_S | 80_F | 1.041 | 0.66 |
| 77_I | 193_A | 1.039 | 0.65 |
| 17_Q | 21_S | 1.038 | 0.65 |
| 33_G | 95_A | 1.038 | 0.65 |
| 28_E | 31_S | 1.028 | 0.64 |
| 7_L | 10_P | 1.027 | 0.64 |
| 23_T | 75_Q | 1.021 | 0.63 |
| 119_T | 151_F | 1.020 | 0.63 |
| 157_G | 160_K | 1.019 | 0.63 |
| 8_L | 29_K | 1.019 | 0.63 |
| 187_L | 216_I | 1.018 | 0.63 |
| 202_C | 217_L | 1.017 | 0.63 |
| 46_V | 66_N | 1.014 | 0.63 |
| 10_P | 23_T | 1.010 | 0.62 |
| 121_D | 186_P | 1.003 | 0.61 |
| 39_I | 190_L | 1.002 | 0.61 |
| 208_H | 212_A | 1.001 | 0.61 |
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 | |
| 3e8tA | 1 | 0.8987 | 100 | 0.209 | Contact Map |
| 2rckA | 2 | 0.9119 | 100 | 0.226 | Contact Map |
| 2rqfA | 1 | 0.9207 | 100 | 0.362 | Contact Map |
| 3uv1A | 2 | 0.7533 | 99.2 | 0.769 | Contact Map |
| 4m4dA | 2 | 0.8546 | 94.9 | 0.892 | Contact Map |
| 1ewfA | 1 | 0.8767 | 94.7 | 0.893 | Contact Map |
| 2obdA | 1 | 0.8546 | 76 | 0.923 | Contact Map |
| 3zpmA | 1 | 0.8414 | 37 | 0.94 | Contact Map |
| 4iwkA | 6 | 0.2643 | 5.1 | 0.96 | Contact Map |
| 4kghB | 2 | 0.8106 | 4.9 | 0.96 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)