| 1g2e |
| ID: | 1408343696 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 167 (165) | ||
| Sequences: | 8534 (5811.2) | ||
| Seq/Len: | 51.721 | ||
| Nf(neff/√len): | 452.4 |
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: 51.721).
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 |
| 28_E | 52_I | 2.975 | 1.00 |
| 139_K | 142_E | 2.936 | 1.00 |
| 53_D | 56_D | 2.864 | 1.00 |
| 114_R | 138_D | 2.574 | 1.00 |
| 18_E | 70_Q | 2.200 | 1.00 |
| 101_T | 104_E | 2.169 | 1.00 |
| 12_Q | 72_K | 2.114 | 1.00 |
| 59_K | 63_T | 2.071 | 1.00 |
| 19_F | 47_G | 2.029 | 1.00 |
| 91_L | 147_I | 2.023 | 1.00 |
| 26_I | 63_T | 2.002 | 1.00 |
| 5_L | 61_I | 1.956 | 1.00 |
| 112_Y | 149_G | 1.933 | 1.00 |
| 105_L | 133_G | 1.907 | 1.00 |
| 15_T | 18_E | 1.866 | 1.00 |
| 106_E | 110_S | 1.793 | 1.00 |
| 20_R | 24_G | 1.764 | 1.00 |
| 145_E | 149_G | 1.717 | 1.00 |
| 7_V | 23_F | 1.712 | 1.00 |
| 59_K | 62_N | 1.637 | 1.00 |
| 138_D | 142_E | 1.636 | 1.00 |
| 30_E | 52_I | 1.633 | 1.00 |
| 123_D | 126_T | 1.630 | 1.00 |
| 58_E | 78_Y | 1.626 | 1.00 |
| 102_Q | 106_E | 1.623 | 1.00 |
| 52_I | 56_D | 1.598 | 1.00 |
| 93_V | 109_F | 1.593 | 1.00 |
| 69_L | 74_I | 1.585 | 1.00 |
| 116_I | 138_D | 1.566 | 1.00 |
| 115_I | 135_I | 1.528 | 1.00 |
| 23_F | 49_V | 1.519 | 1.00 |
| 21_S | 24_G | 1.478 | 1.00 |
| 35_V | 46_Y | 1.478 | 1.00 |
| 109_F | 135_I | 1.471 | 1.00 |
| 30_E | 50_N | 1.462 | 1.00 |
| 37_D | 40_T | 1.443 | 1.00 |
| 140_R | 144_E | 1.438 | 1.00 |
| 68_R | 71_T | 1.437 | 1.00 |
| 104_E | 156_S | 1.428 | 1.00 |
| 98_K | 158_A | 1.428 | 1.00 |
| 97_P | 100_M | 1.424 | 1.00 |
| 121_L | 132_V | 1.398 | 0.99 |
| 32_C | 47_G | 1.398 | 0.99 |
| 28_E | 56_D | 1.392 | 0.99 |
| 116_I | 136_R | 1.392 | 0.99 |
| 118_S | 133_G | 1.362 | 0.99 |
| 22_L | 67_L | 1.351 | 0.99 |
| 57_A | 78_Y | 1.347 | 0.99 |
| 34_L | 43_S | 1.346 | 0.99 |
| 68_R | 73_T | 1.340 | 0.99 |
| 154_K | 157_G | 1.334 | 0.99 |
| 8_N | 75_K | 1.322 | 0.99 |
| 54_P | 78_Y | 1.313 | 0.99 |
| 54_P | 58_E | 1.293 | 0.99 |
| 94_S | 163_T | 1.274 | 0.99 |
| 17_E | 21_S | 1.270 | 0.99 |
| 145_E | 148_K | 1.251 | 0.99 |
| 150_L | 153_Q | 1.223 | 0.98 |
| 93_V | 135_I | 1.219 | 0.98 |
| 16_Q | 20_R | 1.218 | 0.98 |
| 55_K | 59_K | 1.207 | 0.98 |
| 13_N | 70_Q | 1.203 | 0.98 |
| 103_K | 107_Q | 1.198 | 0.98 |
| 107_Q | 110_S | 1.194 | 0.98 |
| 8_N | 46_Y | 1.192 | 0.98 |
| 114_R | 142_E | 1.186 | 0.98 |
| 108_L | 153_Q | 1.183 | 0.98 |
| 108_L | 150_L | 1.182 | 0.98 |
| 11_P | 14_M | 1.178 | 0.98 |
| 58_E | 62_N | 1.177 | 0.98 |
| 90_N | 136_R | 1.176 | 0.98 |
| 137_F | 146_A | 1.172 | 0.98 |
| 144_E | 148_K | 1.169 | 0.97 |
| 16_Q | 36_R | 1.152 | 0.97 |
| 26_I | 64_L | 1.137 | 0.97 |
| 34_L | 47_G | 1.131 | 0.97 |
| 51_Y | 60_A | 1.117 | 0.96 |
| 8_N | 94_S | 1.098 | 0.96 |
| 22_L | 25_S | 1.093 | 0.96 |
| 102_Q | 120_I | 1.086 | 0.96 |
| 16_Q | 34_L | 1.080 | 0.95 |
| 12_Q | 45_G | 1.077 | 0.95 |
| 94_S | 132_V | 1.070 | 0.95 |
| 120_I | 129_S | 1.047 | 0.94 |
| 92_Y | 132_V | 1.045 | 0.94 |
| 89_A | 136_R | 1.043 | 0.94 |
| 3_T | 30_E | 1.021 | 0.93 |
| 121_L | 134_F | 1.020 | 0.93 |
| 142_E | 146_A | 1.019 | 0.93 |
| 29_I | 49_V | 1.003 | 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
- 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 | |
| 1fxlA | 1 | 1 | 100 | 0.089 | Contact Map |
| 1b7fA | 2 | 1 | 100 | 0.091 | Contact Map |
| 2qfjA | 2 | 0.988 | 100 | 0.093 | Contact Map |
| 4f02A | 2 | 0.9701 | 100 | 0.125 | Contact Map |
| 2mjnA | 1 | 0.9521 | 100 | 0.129 | Contact Map |
| 1l3kA | 1 | 0.9461 | 100 | 0.138 | Contact Map |
| 3md3A | 1 | 0.9641 | 100 | 0.141 | Contact Map |
| 2cjkA | 1 | 0.9701 | 100 | 0.142 | Contact Map |
| 3vajA | 2 | 0.9461 | 100 | 0.143 | Contact Map |
| 3nmrA | 1 | 0.982 | 100 | 0.148 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)