| cd81H |
| ID: | 1444728055 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 236 (229) | ||
| Sequences: | 3063 (1970.9) | ||
| Seq/Len: | 13.376 | ||
| Nf(neff/√len): | 130.2 |
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: 13.376).
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 |
| 171_K | 174_L | 4.583 | 1.00 |
| 207_I | 211_V | 3.917 | 1.00 |
| 89_C | 93_T | 3.093 | 1.00 |
| 33_L | 37_H | 2.901 | 1.00 |
| 105_E | 216_M | 2.793 | 1.00 |
| 11_K | 86_E | 2.727 | 1.00 |
| 148_K | 151_H | 2.705 | 1.00 |
| 188_E | 193_K | 2.687 | 1.00 |
| 107_A | 111_W | 2.600 | 1.00 |
| 113_F | 206_G | 2.344 | 1.00 |
| 26_G | 30_G | 2.336 | 1.00 |
| 63_Y | 67_A | 2.295 | 1.00 |
| 29_L | 33_L | 2.170 | 1.00 |
| 18_N | 94_F | 2.083 | 1.00 |
| 95_F | 220_M | 2.044 | 1.00 |
| 92_G | 96_T | 2.026 | 1.00 |
| 30_G | 34_W | 1.984 | 1.00 |
| 12_Y | 15_F | 1.983 | 1.00 |
| 151_H | 158_G | 1.902 | 1.00 |
| 170_L | 174_L | 1.879 | 1.00 |
| 32_A | 69_G | 1.850 | 1.00 |
| 25_G | 69_G | 1.827 | 1.00 |
| 77_F | 81_Y | 1.826 | 1.00 |
| 151_H | 165_L | 1.800 | 1.00 |
| 110_I | 114_V | 1.765 | 1.00 |
| 220_M | 224_M | 1.725 | 1.00 |
| 22_W | 76_G | 1.710 | 1.00 |
| 25_G | 72_M | 1.672 | 1.00 |
| 219_E | 226_L | 1.639 | 1.00 |
| 32_A | 62_I | 1.622 | 1.00 |
| 23_L | 27_V | 1.594 | 1.00 |
| 99_V | 220_M | 1.587 | 1.00 |
| 170_L | 173_N | 1.580 | 1.00 |
| 9_C | 13_L | 1.565 | 1.00 |
| 34_W | 63_Y | 1.548 | 1.00 |
| 15_F | 18_N | 1.524 | 1.00 |
| 223_S | 226_L | 1.470 | 1.00 |
| 151_H | 173_N | 1.461 | 1.00 |
| 204_L | 208_A | 1.448 | 1.00 |
| 79_G | 82_G | 1.445 | 1.00 |
| 30_G | 33_L | 1.440 | 1.00 |
| 147_V | 159_S | 1.439 | 1.00 |
| 92_G | 227_C | 1.438 | 1.00 |
| 225_V | 229_G | 1.428 | 1.00 |
| 81_Y | 90_L | 1.409 | 1.00 |
| 29_L | 70_A | 1.404 | 0.99 |
| 113_F | 210_I | 1.404 | 0.99 |
| 18_N | 21_F | 1.374 | 0.99 |
| 188_E | 196_D | 1.363 | 0.99 |
| 159_S | 191_H | 1.359 | 0.99 |
| 80_C | 86_E | 1.357 | 0.99 |
| 170_L | 176_P | 1.355 | 0.99 |
| 88_Q | 92_G | 1.343 | 0.99 |
| 28_I | 65_L | 1.336 | 0.99 |
| 15_F | 19_F | 1.319 | 0.99 |
| 108_A | 112_G | 1.314 | 0.99 |
| 16_V | 20_V | 1.298 | 0.99 |
| 191_H | 195_D | 1.296 | 0.99 |
| 219_E | 223_S | 1.286 | 0.99 |
| 202_L | 205_I | 1.280 | 0.99 |
| 109_G | 213_A | 1.273 | 0.99 |
| 171_K | 176_P | 1.271 | 0.99 |
| 95_F | 99_V | 1.263 | 0.99 |
| 147_V | 151_H | 1.260 | 0.99 |
| 95_F | 224_M | 1.249 | 0.99 |
| 203_Y | 207_I | 1.248 | 0.99 |
| 11_K | 15_F | 1.240 | 0.98 |
| 14_L | 18_N | 1.236 | 0.98 |
| 22_W | 73_M | 1.234 | 0.98 |
| 166_T | 169_V | 1.230 | 0.98 |
| 102_F | 220_M | 1.226 | 0.98 |
| 18_N | 22_W | 1.224 | 0.98 |
| 36_R | 66_I | 1.223 | 0.98 |
| 148_K | 171_K | 1.201 | 0.98 |
| 82_G | 90_L | 1.175 | 0.98 |
| 34_W | 38_D | 1.175 | 0.98 |
| 158_G | 164_A | 1.166 | 0.97 |
| 82_G | 91_L | 1.163 | 0.97 |
| 148_K | 189_D | 1.161 | 0.97 |
| 206_G | 210_I | 1.151 | 0.97 |
| 77_F | 80_C | 1.148 | 0.97 |
| 151_H | 156_C | 1.138 | 0.97 |
| 25_G | 29_L | 1.138 | 0.97 |
| 11_K | 14_L | 1.130 | 0.97 |
| 158_G | 161_T | 1.130 | 0.97 |
| 224_M | 227_C | 1.129 | 0.97 |
| 224_M | 228_C | 1.115 | 0.96 |
| 165_L | 173_N | 1.113 | 0.96 |
| 26_G | 73_M | 1.096 | 0.96 |
| 219_E | 222_L | 1.093 | 0.96 |
| 155_D | 186_F | 1.089 | 0.96 |
| 213_A | 219_E | 1.081 | 0.95 |
| 102_F | 217_I | 1.079 | 0.95 |
| 106_V | 110_I | 1.077 | 0.95 |
| 95_F | 227_C | 1.073 | 0.95 |
| 127_Y | 130_A | 1.060 | 0.95 |
| 22_W | 77_F | 1.058 | 0.95 |
| 11_K | 18_N | 1.055 | 0.95 |
| 78_L | 93_T | 1.049 | 0.94 |
| 166_T | 170_L | 1.030 | 0.94 |
| 30_G | 37_H | 1.016 | 0.93 |
| 79_G | 94_F | 1.015 | 0.93 |
| 226_L | 230_I | 1.008 | 0.93 |
| 61_G | 94_F | 1.007 | 0.93 |
| 225_V | 228_C | 1.004 | 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
- 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 | |
| 3x0fA | 2 | 0 | 99.5 | 0.653 | Contact Map |
| 2m7zA | 1 | 0.3432 | 99.3 | 0.684 | Contact Map |
| 2ks1B | 1 | 0.1864 | 11.5 | 0.94 | Contact Map |
| 2kluA | 1 | 0.1695 | 6.7 | 0.946 | Contact Map |
| 2jwaA | 2 | 0.1864 | 4.7 | 0.95 | Contact Map |
| 2m35A | 1 | 0.2203 | 3.5 | 0.952 | Contact Map |
| 4pxzA | 1 | 0.1907 | 3.5 | 0.952 | Contact Map |
| 4mbsA | 2 | 0.1907 | 3.2 | 0.954 | Contact Map |
| 4b1qP | 1 | 0.1144 | 3 | 0.954 | Contact Map |
| 2kncB | 1 | 0.1864 | 2.8 | 0.955 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)