| comb 1-170 |
| ID: | 1490708133 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 170 (161) | ||
| Sequences: | 2061 (1385) | ||
| Seq/Len: | 12.801 | ||
| Nf(neff/√len): | 109.2 |
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: 12.801).
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 |
| 19_D | 152_G | 3.568 | 1.00 |
| 66_F | 98_A | 3.558 | 1.00 |
| 56_R | 97_E | 3.085 | 1.00 |
| 22_P | 25_R | 2.782 | 1.00 |
| 99_K | 103_K | 2.630 | 1.00 |
| 54_D | 57_Y | 2.452 | 1.00 |
| 60_D | 101_F | 2.378 | 1.00 |
| 56_R | 60_D | 2.350 | 1.00 |
| 31_T | 58_Q | 2.152 | 1.00 |
| 31_T | 34_S | 2.094 | 1.00 |
| 150_K | 153_D | 1.990 | 1.00 |
| 56_R | 100_Q | 1.965 | 1.00 |
| 12_K | 105_N | 1.940 | 1.00 |
| 109_T | 151_L | 1.912 | 1.00 |
| 102_L | 108_E | 1.881 | 1.00 |
| 59_M | 66_F | 1.870 | 1.00 |
| 113_S | 163_R | 1.869 | 1.00 |
| 90_T | 93_E | 1.850 | 1.00 |
| 33_D | 50_T | 1.782 | 1.00 |
| 28_I | 65_I | 1.743 | 1.00 |
| 33_D | 69_R | 1.670 | 1.00 |
| 80_L | 91_L | 1.653 | 1.00 |
| 30_G | 65_I | 1.613 | 1.00 |
| 21_I | 25_R | 1.592 | 1.00 |
| 102_L | 159_V | 1.581 | 1.00 |
| 68_I | 94_F | 1.576 | 1.00 |
| 98_A | 158_I | 1.553 | 1.00 |
| 34_S | 58_Q | 1.516 | 1.00 |
| 55_F | 66_F | 1.508 | 1.00 |
| 151_L | 155_R | 1.508 | 1.00 |
| 73_T | 79_V | 1.499 | 1.00 |
| 98_A | 112_M | 1.494 | 1.00 |
| 69_R | 82_H | 1.483 | 1.00 |
| 98_A | 110_I | 1.463 | 1.00 |
| 50_T | 69_R | 1.380 | 0.99 |
| 35_G | 55_F | 1.374 | 0.99 |
| 58_Q | 64_R | 1.352 | 0.99 |
| 68_I | 112_M | 1.352 | 0.99 |
| 59_M | 110_I | 1.309 | 0.99 |
| 68_I | 80_L | 1.278 | 0.99 |
| 113_S | 117_E | 1.272 | 0.99 |
| 100_Q | 104_D | 1.271 | 0.99 |
| 12_K | 15_Q | 1.267 | 0.99 |
| 11_S | 105_N | 1.266 | 0.99 |
| 7_L | 10_W | 1.264 | 0.99 |
| 155_R | 158_I | 1.260 | 0.99 |
| 12_K | 18_P | 1.254 | 0.99 |
| 53_Y | 61_H | 1.227 | 0.98 |
| 30_G | 67_D | 1.221 | 0.98 |
| 55_F | 58_Q | 1.209 | 0.98 |
| 32_H | 82_H | 1.206 | 0.98 |
| 33_D | 82_H | 1.201 | 0.98 |
| 59_M | 101_F | 1.194 | 0.98 |
| 23_L | 111_I | 1.192 | 0.98 |
| 60_D | 104_D | 1.187 | 0.98 |
| 58_Q | 63_A | 1.179 | 0.98 |
| 101_F | 108_E | 1.164 | 0.97 |
| 12_K | 16_P | 1.159 | 0.97 |
| 70_G | 128_F | 1.159 | 0.97 |
| 71_R | 81_H | 1.153 | 0.97 |
| 15_Q | 107_S | 1.134 | 0.97 |
| 100_Q | 103_K | 1.132 | 0.97 |
| 143_L | 147_G | 1.128 | 0.97 |
| 60_D | 105_N | 1.095 | 0.96 |
| 80_L | 94_F | 1.088 | 0.96 |
| 37_F | 54_D | 1.085 | 0.96 |
| 9_N | 12_K | 1.081 | 0.95 |
| 69_R | 115_K | 1.076 | 0.95 |
| 13_W | 29_P | 1.038 | 0.94 |
| 79_V | 90_T | 1.029 | 0.94 |
| 51_Q | 62_G | 1.024 | 0.93 |
| 37_F | 87_L | 1.023 | 0.93 |
| 17_I | 21_I | 1.020 | 0.93 |
| 65_I | 113_S | 1.015 | 0.93 |
| 91_L | 95_I | 1.012 | 0.93 |
| 18_P | 21_I | 1.005 | 0.93 |
| 93_E | 96_N | 1.002 | 0.92 |
| 91_L | 114_L | 1.002 | 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
- 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 | |
| 3ea1A | 2 | 1 | 100 | 0.107 | Contact Map |
| 2plcA | 1 | 0.9353 | 100 | 0.157 | Contact Map |
| 4i90A | 1 | 0.9824 | 100 | 0.172 | Contact Map |
| 3h4xA | 1 | 0.8176 | 100 | 0.364 | Contact Map |
| 2zkmX | 1 | 0.9412 | 98.9 | 0.728 | Contact Map |
| 1djxA | 2 | 0.9588 | 98.8 | 0.733 | Contact Map |
| 3ohmB | 1 | 0.9471 | 98.8 | 0.736 | Contact Map |
| 4gnkB | 2 | 0.9412 | 98.8 | 0.736 | Contact Map |
| 3qr0A | 1 | 0.9471 | 98.8 | 0.739 | Contact Map |
| 1vd6A | 1 | 0.7882 | 76.4 | 0.897 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)