| BPGM |
| ID: | 1467829221 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 264 (222) | ||
| Sequences: | 1690 (895.4) | ||
| Seq/Len: | 7.613 | ||
| Nf(neff/√len): | 60.1 |
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: 7.613).
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 |
| 14_L | 75_I | 3.899 | 1.00 |
| 18_E | 38_E | 3.577 | 1.00 |
| 60_V | 72_A | 3.433 | 1.00 |
| 130_P | 160_S | 3.132 | 1.00 |
| 124_Y | 167_L | 2.850 | 1.00 |
| 202_K | 209_D | 2.747 | 1.00 |
| 59_L | 87_E | 2.584 | 1.00 |
| 201_L | 217_L | 2.540 | 1.00 |
| 208_S | 211_D | 2.410 | 1.00 |
| 205_E | 225_L | 2.369 | 1.00 |
| 34_K | 70_H | 2.324 | 1.00 |
| 20_A | 24_E | 2.309 | 1.00 |
| 127_T | 165_D | 2.269 | 1.00 |
| 162_S | 165_D | 2.231 | 1.00 |
| 10_K | 226_E | 2.205 | 1.00 |
| 48_K | 78_E | 2.143 | 1.00 |
| 73_W | 82_E | 2.140 | 1.00 |
| 153_P | 156_Q | 2.105 | 1.00 |
| 207_I | 211_D | 2.067 | 1.00 |
| 61_F | 181_E | 2.015 | 1.00 |
| 37_S | 40_M | 2.008 | 1.00 |
| 12_I | 57_F | 2.002 | 1.00 |
| 228_D | 232_R | 1.996 | 1.00 |
| 146_R | 149_V | 1.996 | 1.00 |
| 50_L | 55_F | 1.919 | 1.00 |
| 70_H | 77_E | 1.910 | 1.00 |
| 207_I | 212_I | 1.881 | 1.00 |
| 118_R | 214_N | 1.877 | 1.00 |
| 45_N | 48_K | 1.869 | 1.00 |
| 103_L | 108_M | 1.863 | 1.00 |
| 164_K | 168_E | 1.857 | 1.00 |
| 59_L | 188_I | 1.856 | 1.00 |
| 149_V | 152_V | 1.849 | 1.00 |
| 131_I | 135_H | 1.843 | 1.00 |
| 60_V | 84_V | 1.809 | 1.00 |
| 28_C | 33_Q | 1.797 | 1.00 |
| 44_R | 78_E | 1.797 | 1.00 |
| 48_K | 52_A | 1.793 | 1.00 |
| 61_F | 173_Y | 1.790 | 1.00 |
| 179_A | 231_L | 1.770 | 1.00 |
| 41_E | 44_R | 1.764 | 1.00 |
| 34_K | 66_N | 1.744 | 1.00 |
| 181_E | 184_R | 1.736 | 1.00 |
| 125_N | 164_K | 1.731 | 1.00 |
| 103_L | 111_N | 1.704 | 1.00 |
| 119_L | 123_S | 1.696 | 1.00 |
| 42_E | 219_T | 1.629 | 1.00 |
| 133_E | 159_R | 1.626 | 1.00 |
| 109_A | 117_V | 1.608 | 1.00 |
| 131_I | 137_Y | 1.607 | 1.00 |
| 73_W | 86_V | 1.606 | 1.00 |
| 31_V | 137_Y | 1.587 | 1.00 |
| 70_H | 82_E | 1.536 | 1.00 |
| 192_A | 196_S | 1.512 | 0.99 |
| 47_G | 78_E | 1.511 | 0.99 |
| 106_E | 109_A | 1.509 | 0.99 |
| 44_R | 74_L | 1.495 | 0.99 |
| 138_Y | 159_R | 1.485 | 0.99 |
| 55_F | 187_T | 1.485 | 0.99 |
| 40_M | 74_L | 1.480 | 0.99 |
| 165_D | 168_E | 1.472 | 0.99 |
| 171_L | 203_H | 1.462 | 0.99 |
| 227_L | 231_L | 1.454 | 0.99 |
| 40_M | 70_H | 1.444 | 0.99 |
| 50_L | 79_L | 1.435 | 0.99 |
| 18_E | 23_K | 1.414 | 0.99 |
| 178_I | 190_I | 1.408 | 0.99 |
| 66_N | 80_G | 1.395 | 0.99 |
| 148_K | 152_V | 1.388 | 0.99 |
| 147_Y | 150_C | 1.375 | 0.99 |
| 18_E | 36_N | 1.373 | 0.99 |
| 127_T | 130_P | 1.337 | 0.98 |
| 56_E | 187_T | 1.330 | 0.98 |
| 139_Q | 157_L | 1.317 | 0.98 |
| 152_V | 157_L | 1.302 | 0.98 |
| 57_F | 187_T | 1.299 | 0.98 |
| 87_E | 177_R | 1.284 | 0.98 |
| 177_R | 181_E | 1.235 | 0.97 |
| 69_I | 83_W | 1.233 | 0.97 |
| 40_M | 44_R | 1.213 | 0.97 |
| 80_G | 83_W | 1.199 | 0.96 |
| 133_E | 154_L | 1.196 | 0.96 |
| 149_V | 154_L | 1.181 | 0.96 |
| 37_S | 41_E | 1.179 | 0.96 |
| 109_A | 114_E | 1.176 | 0.96 |
| 31_V | 101_I | 1.168 | 0.96 |
| 108_M | 112_H | 1.156 | 0.95 |
| 31_V | 135_H | 1.140 | 0.95 |
| 25_N | 104_N | 1.136 | 0.95 |
| 166_V | 196_S | 1.126 | 0.94 |
| 38_E | 41_E | 1.108 | 0.94 |
| 123_S | 126_V | 1.107 | 0.94 |
| 50_L | 75_I | 1.105 | 0.94 |
| 204_L | 227_L | 1.103 | 0.94 |
| 162_S | 167_L | 1.092 | 0.93 |
| 170_L | 200_L | 1.068 | 0.92 |
| 207_I | 215_I | 1.047 | 0.91 |
| 61_F | 177_R | 1.046 | 0.91 |
| 70_H | 73_W | 1.044 | 0.91 |
| 149_V | 153_P | 1.042 | 0.91 |
| 64_V | 85_P | 1.021 | 0.90 |
| 133_E | 138_Y | 1.020 | 0.89 |
| 150_C | 153_P | 1.016 | 0.89 |
| 100_L | 120_W | 1.001 | 0.88 |
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 | |
| 2hhjA | 2 | 0.9621 | 100 | 0.295 | Contact Map |
| 1riiA | 4 | 0.9167 | 100 | 0.317 | Contact Map |
| 4odiA | 4 | 0.9394 | 100 | 0.335 | Contact Map |
| 3d8hA | 2 | 0.8902 | 100 | 0.395 | Contact Map |
| 3kkkA | 4 | 0.875 | 100 | 0.401 | Contact Map |
| 3gp3A | 4 | 0.8712 | 100 | 0.404 | Contact Map |
| 4gpzA | 2 | 0.9129 | 100 | 0.405 | Contact Map |
| 1e58A | 1 | 0.9318 | 100 | 0.414 | Contact Map |
| 1qhfA | 2 | 0.9091 | 100 | 0.418 | Contact Map |
| 4embA | 4 | 0.928 | 100 | 0.426 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)