| liph-m1 |
| ID: | 1446131100 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 243 (211) | ||
| Sequences: | 826 (515.4) | ||
| Seq/Len: | 3.915 | ||
| Nf(neff/√len): | 35.5 |
HHblits Results: (2015_06)
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: 3.915).
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 |
| 205_H | 221_L | 3.703 | 1.00 |
| 149_Y | 175_T | 3.138 | 1.00 |
| 175_T | 202_D | 2.864 | 1.00 |
| 173_R | 202_D | 2.711 | 1.00 |
| 203_V | 218_G | 2.552 | 1.00 |
| 149_Y | 173_R | 2.544 | 1.00 |
| 149_Y | 202_D | 2.529 | 1.00 |
| 75_V | 160_S | 2.386 | 1.00 |
| 120_A | 123_K | 2.363 | 1.00 |
| 164_G | 174_I | 2.313 | 1.00 |
| 143_A | 148_I | 2.091 | 1.00 |
| 66_N | 69_K | 1.923 | 1.00 |
| 128_A | 132_K | 1.911 | 1.00 |
| 69_K | 100_D | 1.894 | 1.00 |
| 203_V | 221_L | 1.889 | 1.00 |
| 176_G | 193_L | 1.866 | 1.00 |
| 128_A | 163_V | 1.864 | 1.00 |
| 111_G | 123_K | 1.810 | 1.00 |
| 150_M | 160_S | 1.780 | 0.99 |
| 232_L | 235_N | 1.739 | 0.99 |
| 48_R | 100_D | 1.732 | 0.99 |
| 128_A | 162_F | 1.690 | 0.99 |
| 204_I | 222_L | 1.676 | 0.99 |
| 151_I | 177_L | 1.675 | 0.99 |
| 136_D | 167_Y | 1.662 | 0.99 |
| 65_L | 71_T | 1.516 | 0.98 |
| 71_T | 102_N | 1.500 | 0.97 |
| 157_A | 176_G | 1.476 | 0.97 |
| 227_I | 235_N | 1.474 | 0.97 |
| 173_R | 200_F | 1.469 | 0.97 |
| 72_T | 101_M | 1.462 | 0.97 |
| 227_I | 233_P | 1.457 | 0.97 |
| 132_K | 166_M | 1.450 | 0.97 |
| 175_T | 200_F | 1.446 | 0.97 |
| 87_W | 91_L | 1.431 | 0.96 |
| 208_T | 214_K | 1.429 | 0.96 |
| 227_I | 234_Q | 1.385 | 0.95 |
| 213_Y | 217_L | 1.372 | 0.95 |
| 179_P | 203_V | 1.360 | 0.95 |
| 174_I | 193_L | 1.354 | 0.95 |
| 65_L | 102_N | 1.354 | 0.95 |
| 70_K | 147_D | 1.320 | 0.94 |
| 201_V | 218_G | 1.317 | 0.93 |
| 71_T | 104_V | 1.307 | 0.93 |
| 39_L | 111_G | 1.295 | 0.93 |
| 228_G | 233_P | 1.279 | 0.92 |
| 228_G | 235_N | 1.278 | 0.92 |
| 45_L | 102_N | 1.273 | 0.92 |
| 124_T | 159_I | 1.259 | 0.91 |
| 106_V | 131_L | 1.243 | 0.91 |
| 132_K | 163_V | 1.242 | 0.91 |
| 108_W | 112_A | 1.241 | 0.91 |
| 95_L | 101_M | 1.238 | 0.90 |
| 150_M | 163_V | 1.236 | 0.90 |
| 193_L | 203_V | 1.233 | 0.90 |
| 132_K | 167_Y | 1.220 | 0.90 |
| 146_D | 199_Q | 1.220 | 0.90 |
| 78_F | 115_L | 1.213 | 0.89 |
| 41_V | 130_V | 1.199 | 0.88 |
| 203_V | 217_L | 1.198 | 0.88 |
| 152_G | 156_G | 1.192 | 0.88 |
| 154_S | 180_A | 1.189 | 0.88 |
| 201_V | 221_L | 1.186 | 0.88 |
| 164_G | 181_G | 1.173 | 0.87 |
| 170_W | 199_Q | 1.165 | 0.86 |
| 227_I | 232_L | 1.161 | 0.86 |
| 115_L | 153_V | 1.161 | 0.86 |
| 60_S | 63_G | 1.155 | 0.86 |
| 229_S | 233_P | 1.145 | 0.85 |
| 179_P | 217_L | 1.118 | 0.83 |
| 216_P | 223_P | 1.112 | 0.83 |
| 73_F | 135_I | 1.112 | 0.83 |
| 120_A | 155_L | 1.101 | 0.82 |
| 131_L | 163_V | 1.100 | 0.82 |
| 47_T | 63_G | 1.092 | 0.81 |
| 27_R | 32_S | 1.092 | 0.81 |
| 74_I | 91_L | 1.090 | 0.81 |
| 88_M | 91_L | 1.079 | 0.80 |
| 47_T | 50_N | 1.079 | 0.80 |
| 181_G | 213_Y | 1.076 | 0.80 |
| 192_R | 197_D | 1.070 | 0.79 |
| 200_F | 220_R | 1.063 | 0.79 |
| 174_I | 197_D | 1.060 | 0.78 |
| 27_R | 30_F | 1.052 | 0.78 |
| 124_T | 162_F | 1.041 | 0.77 |
| 201_V | 205_H | 1.037 | 0.76 |
| 229_S | 235_N | 1.037 | 0.76 |
| 149_Y | 200_F | 1.026 | 0.75 |
| 47_T | 64_N | 1.024 | 0.75 |
| 109_N | 112_A | 1.023 | 0.75 |
| 72_T | 175_T | 1.022 | 0.75 |
| 158_H | 161_G | 1.022 | 0.75 |
| 117_Y | 180_A | 1.019 | 0.74 |
| 129_M | 166_M | 1.017 | 0.74 |
| 194_D | 197_D | 1.013 | 0.74 |
| 39_L | 125_R | 1.005 | 0.73 |
| 75_V | 131_L | 1.004 | 0.73 |
| 158_H | 207_D | 1.002 | 0.73 |
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 | |
| 1hplA | 2 | 0.9671 | 100 | 0.471 | Contact Map |
| 1w52X | 1 | 0.9506 | 100 | 0.472 | Contact Map |
| 1rp1A | 1 | 0.963 | 100 | 0.478 | Contact Map |
| 1bu8A | 1 | 0.9671 | 100 | 0.484 | Contact Map |
| 1gplA | 1 | 0.9671 | 100 | 0.5 | Contact Map |
| 4qnnA | 4 | 0 | 100 | 0.513 | Contact Map |
| 3styA | 2 | 0.6872 | 98.9 | 0.861 | Contact Map |
| 3dqzA | 4 | 0.6914 | 98.8 | 0.864 | Contact Map |
| 2wflA | 1 | 0.679 | 98.8 | 0.865 | Contact Map |
| 3c6xA | 1 | 0.6872 | 98.7 | 0.866 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)