| Test1 |
| ID: | 1504545622 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 140 (116) | ||
| Sequences: | 40183 (27430) | ||
| Seq/Len: | 346.405 | ||
| Nf(neff/√len): | 2546.8 |
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: 346.405).
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 |
| 12_A | 34_C | 2.944 | 1.00 |
| 33_T | 76_Y | 2.723 | 1.00 |
| 39_T | 59_L | 2.384 | 1.00 |
| 33_T | 58_Q | 2.347 | 1.00 |
| 102_L | 106_G | 2.344 | 1.00 |
| 6_R | 31_A | 2.197 | 1.00 |
| 5_M | 78_V | 2.026 | 1.00 |
| 8_L | 76_Y | 2.025 | 1.00 |
| 45_A | 57_C | 1.995 | 1.00 |
| 77_D | 103_A | 1.900 | 1.00 |
| 31_A | 56_Q | 1.878 | 1.00 |
| 6_R | 33_T | 1.779 | 1.00 |
| 33_T | 56_Q | 1.769 | 1.00 |
| 18_T | 32_Y | 1.757 | 1.00 |
| 86_H | 112_E | 1.704 | 1.00 |
| 37_H | 61_D | 1.701 | 1.00 |
| 19_E | 49_F | 1.645 | 1.00 |
| 35_T | 60_L | 1.629 | 1.00 |
| 81_A | 84_S | 1.606 | 1.00 |
| 98_A | 108_L | 1.587 | 1.00 |
| 42_L | 46_K | 1.544 | 1.00 |
| 42_L | 57_C | 1.544 | 1.00 |
| 42_L | 59_L | 1.538 | 1.00 |
| 11_G | 84_S | 1.538 | 1.00 |
| 97_H | 100_S | 1.526 | 1.00 |
| 79_I | 102_L | 1.513 | 1.00 |
| 6_R | 77_D | 1.490 | 1.00 |
| 18_T | 34_C | 1.435 | 1.00 |
| 6_R | 76_Y | 1.435 | 1.00 |
| 2_G | 5_M | 1.428 | 1.00 |
| 39_T | 43_Q | 1.424 | 1.00 |
| 79_I | 98_A | 1.369 | 0.99 |
| 10_I | 98_A | 1.313 | 0.99 |
| 7_I | 78_V | 1.302 | 0.99 |
| 97_H | 101_L | 1.300 | 0.99 |
| 87_R | 112_E | 1.293 | 0.99 |
| 92_G | 96_S | 1.288 | 0.99 |
| 19_E | 48_R | 1.256 | 0.99 |
| 25_L | 30_A | 1.248 | 0.99 |
| 83_D | 86_H | 1.232 | 0.98 |
| 102_L | 108_L | 1.226 | 0.98 |
| 36_D | 42_L | 1.207 | 0.98 |
| 6_R | 75_Q | 1.180 | 0.98 |
| 83_D | 111_L | 1.165 | 0.97 |
| 72_E | 75_Q | 1.161 | 0.97 |
| 26_P | 29_V | 1.153 | 0.97 |
| 88_A | 94_A | 1.152 | 0.97 |
| 78_V | 107_V | 1.152 | 0.97 |
| 71_Y | 76_Y | 1.140 | 0.97 |
| 23_A | 52_L | 1.128 | 0.97 |
| 90_D | 93_V | 1.123 | 0.97 |
| 86_H | 113_L | 1.113 | 0.96 |
| 49_F | 57_C | 1.109 | 0.96 |
| 10_I | 62_M | 1.106 | 0.96 |
| 17_L | 82_A | 1.101 | 0.96 |
| 6_R | 103_A | 1.094 | 0.96 |
| 34_C | 57_C | 1.091 | 0.96 |
| 36_D | 41_F | 1.091 | 0.96 |
| 12_A | 18_T | 1.080 | 0.95 |
| 84_S | 88_A | 1.066 | 0.95 |
| 73_A | 100_S | 1.055 | 0.95 |
| 93_V | 96_S | 1.048 | 0.94 |
| 78_V | 109_I | 1.014 | 0.93 |
| 82_A | 111_L | 1.013 | 0.93 |
| 4_P | 30_A | 1.009 | 0.93 |
| 8_L | 79_I | 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 | |
| 4pivA | 2 | 0.8929 | 99.6 | 0.142 | Contact Map |
| 4kvzA | 1 | 0.9286 | 99.5 | 0.196 | Contact Map |
| 3mggA | 2 | 0.9571 | 99.4 | 0.215 | Contact Map |
| 4pneA | 2 | 0.9286 | 99.4 | 0.218 | Contact Map |
| 3busA | 2 | 0.9429 | 99.4 | 0.218 | Contact Map |
| 4krgA | 2 | 0.9143 | 99.4 | 0.22 | Contact Map |
| 4kwcA | 1 | 0.9286 | 99.4 | 0.224 | Contact Map |
| 4ineA | 2 | 0.9429 | 99.4 | 0.225 | Contact Map |
| 2o57A | 4 | 0.9429 | 99.4 | 0.225 | Contact Map |
| 3ujcA | 1 | 0.9429 | 99.4 | 0.227 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)