| BepA 15-235 |
| ID: | 1507223372 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 221 (205) | ||
| Sequences: | 2363 (1650.1) | ||
| Seq/Len: | 11.527 | ||
| Nf(neff/√len): | 115.2 |
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: 11.527).
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 |
| 51_T | 72_L | 4.091 | 1.00 |
| 135_I | 197_Q | 2.981 | 1.00 |
| 55_C | 147_F | 2.517 | 1.00 |
| 72_L | 109_L | 2.427 | 1.00 |
| 142_N | 155_Q | 2.348 | 1.00 |
| 119_K | 133_E | 2.142 | 1.00 |
| 108_G | 111_R | 2.113 | 1.00 |
| 139_N | 187_V | 2.087 | 1.00 |
| 132_S | 197_Q | 2.056 | 1.00 |
| 152_G | 156_R | 2.052 | 1.00 |
| 76_P | 102_G | 1.896 | 1.00 |
| 56_H | 59_Q | 1.836 | 1.00 |
| 110_Q | 114_Q | 1.781 | 1.00 |
| 104_E | 107_E | 1.747 | 1.00 |
| 105_I | 144_L | 1.739 | 1.00 |
| 116_L | 162_L | 1.693 | 1.00 |
| 104_E | 108_G | 1.667 | 1.00 |
| 73_R | 77_F | 1.645 | 1.00 |
| 145_H | 152_G | 1.637 | 1.00 |
| 176_T | 179_R | 1.629 | 1.00 |
| 180_M | 184_S | 1.617 | 1.00 |
| 136_E | 193_L | 1.607 | 1.00 |
| 56_H | 60_Q | 1.606 | 1.00 |
| 186_A | 195_P | 1.605 | 1.00 |
| 21_N | 24_A | 1.567 | 1.00 |
| 142_N | 152_G | 1.563 | 1.00 |
| 36_A | 63_K | 1.557 | 1.00 |
| 145_H | 153_R | 1.525 | 1.00 |
| 155_Q | 159_F | 1.499 | 1.00 |
| 198_H | 202_D | 1.497 | 1.00 |
| 106_Q | 110_Q | 1.483 | 1.00 |
| 51_T | 106_Q | 1.476 | 1.00 |
| 134_A | 200_F | 1.469 | 1.00 |
| 73_R | 105_I | 1.435 | 1.00 |
| 36_A | 39_N | 1.433 | 1.00 |
| 47_E | 53_Y | 1.428 | 1.00 |
| 50_D | 53_Y | 1.417 | 1.00 |
| 114_Q | 118_E | 1.412 | 1.00 |
| 59_Q | 63_K | 1.412 | 1.00 |
| 33_T | 61_L | 1.409 | 1.00 |
| 68_W | 71_Y | 1.384 | 0.99 |
| 55_C | 71_Y | 1.362 | 0.99 |
| 130_F | 166_A | 1.353 | 0.99 |
| 17_Y | 28_K | 1.342 | 0.99 |
| 109_L | 113_D | 1.333 | 0.99 |
| 149_E | 153_R | 1.309 | 0.99 |
| 209_I | 213_K | 1.307 | 0.99 |
| 99_F | 152_G | 1.300 | 0.99 |
| 7_Y | 11_T | 1.295 | 0.99 |
| 107_E | 110_Q | 1.271 | 0.99 |
| 79_F | 149_E | 1.265 | 0.99 |
| 176_T | 206_P | 1.263 | 0.99 |
| 111_R | 114_Q | 1.262 | 0.99 |
| 102_G | 106_Q | 1.262 | 0.99 |
| 60_Q | 63_K | 1.262 | 0.99 |
| 29_C | 66_F | 1.261 | 0.99 |
| 51_T | 113_D | 1.253 | 0.99 |
| 54_L | 158_F | 1.244 | 0.98 |
| 143_Q | 188_A | 1.241 | 0.98 |
| 5_Y | 10_T | 1.234 | 0.98 |
| 112_L | 144_L | 1.232 | 0.98 |
| 36_A | 60_Q | 1.221 | 0.98 |
| 182_V | 186_A | 1.217 | 0.98 |
| 112_L | 137_L | 1.199 | 0.98 |
| 100_A | 108_G | 1.193 | 0.98 |
| 138_F | 200_F | 1.177 | 0.98 |
| 134_A | 163_A | 1.175 | 0.98 |
| 52_A | 56_H | 1.174 | 0.98 |
| 157_L | 160_E | 1.158 | 0.97 |
| 141_L | 155_Q | 1.153 | 0.97 |
| 36_A | 64_N | 1.138 | 0.97 |
| 109_L | 144_L | 1.131 | 0.97 |
| 57_I | 154_T | 1.120 | 0.96 |
| 139_N | 193_L | 1.118 | 0.96 |
| 210_R | 213_K | 1.100 | 0.96 |
| 205_N | 209_I | 1.099 | 0.96 |
| 133_E | 162_L | 1.088 | 0.96 |
| 138_F | 180_M | 1.084 | 0.96 |
| 54_L | 147_F | 1.077 | 0.95 |
| 141_L | 154_T | 1.075 | 0.95 |
| 130_F | 168_H | 1.073 | 0.95 |
| 76_P | 98_A | 1.062 | 0.95 |
| 138_F | 159_F | 1.051 | 0.94 |
| 136_E | 140_S | 1.046 | 0.94 |
| 113_D | 158_F | 1.042 | 0.94 |
| 119_K | 137_L | 1.039 | 0.94 |
| 68_W | 74_H | 1.037 | 0.94 |
| 105_I | 146_P | 1.036 | 0.94 |
| 51_T | 110_Q | 1.034 | 0.94 |
| 186_A | 192_D | 1.034 | 0.94 |
| 135_I | 196_M | 1.026 | 0.94 |
| 54_L | 113_D | 1.023 | 0.93 |
| 145_H | 149_E | 1.022 | 0.93 |
| 7_Y | 10_T | 1.022 | 0.93 |
| 30_S | 34_A | 1.020 | 0.93 |
| 129_E | 132_S | 1.013 | 0.93 |
| 179_R | 202_D | 1.011 | 0.93 |
| 5_Y | 13_L | 1.003 | 0.93 |
| 108_G | 144_L | 1.001 | 0.92 |
| 36_A | 40_L | 1.000 | 0.92 |
| 185_V | 189_E | 1.000 | 0.92 |
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 | |
| 4n67A | 1 | 0.9638 | 100 | 0.168 | Contact Map |
| 4npsA | 1 | 0.9548 | 100 | 0.168 | Contact Map |
| 2jk8A | 2 | 0.9955 | 100 | 0.173 | Contact Map |
| 4m16A | 1 | 0.9729 | 100 | 0.192 | Contact Map |
| 4py3A | 10 | 0 | 100 | 0.192 | Contact Map |
| 3zc7A | 1 | 0.9005 | 100 | 0.207 | Contact Map |
| 3shgA | 1 | 0.8688 | 100 | 0.23 | Contact Map |
| 4u04A | 2 | 0.8869 | 100 | 0.384 | Contact Map |
| 3cucA | 2 | 0.9231 | 100 | 0.398 | Contact Map |
| 4rglA | 1 | 0.9005 | 100 | 0.411 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)