| dut |
| ID: | 1429968221 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 132 (125) | ||
| Sequences: | 1942 (1249.1) | ||
| Seq/Len: | 15.536 | ||
| Nf(neff/√len): | 111.7 |
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: 15.536).
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 |
| 16_D | 71_G | 3.586 | 1.00 |
| 44_F | 119_K | 3.370 | 1.00 |
| 91_L | 94_H | 3.033 | 1.00 |
| 26_D | 91_L | 2.858 | 1.00 |
| 51_G | 99_L | 2.818 | 1.00 |
| 30_Q | 87_P | 2.713 | 1.00 |
| 18_G | 100_I | 2.652 | 1.00 |
| 61_F | 88_I | 2.581 | 1.00 |
| 19_I | 108_Y | 2.397 | 1.00 |
| 15_Q | 70_V | 2.300 | 1.00 |
| 54_V | 67_I | 2.259 | 1.00 |
| 30_Q | 33_Q | 2.158 | 1.00 |
| 38_K | 77_F | 1.965 | 1.00 |
| 13_Y | 19_I | 1.953 | 1.00 |
| 31_P | 87_P | 1.914 | 1.00 |
| 44_F | 73_T | 1.893 | 1.00 |
| 28_V | 89_N | 1.891 | 1.00 |
| 45_I | 101_L | 1.888 | 1.00 |
| 52_R | 67_I | 1.858 | 1.00 |
| 13_Y | 105_S | 1.834 | 1.00 |
| 33_Q | 85_L | 1.822 | 1.00 |
| 36_K | 77_F | 1.718 | 1.00 |
| 26_D | 92_K | 1.665 | 1.00 |
| 43_V | 51_G | 1.662 | 1.00 |
| 52_R | 102_T | 1.636 | 1.00 |
| 38_K | 75_E | 1.626 | 1.00 |
| 8_K | 92_K | 1.584 | 1.00 |
| 50_Y | 67_I | 1.522 | 1.00 |
| 21_M | 51_G | 1.492 | 1.00 |
| 29_L | 35_T | 1.487 | 1.00 |
| 55_A | 64_I | 1.441 | 1.00 |
| 54_V | 102_T | 1.419 | 1.00 |
| 40_N | 75_E | 1.416 | 1.00 |
| 28_V | 87_P | 1.416 | 1.00 |
| 12_N | 22_Y | 1.410 | 1.00 |
| 23_N | 90_L | 1.398 | 0.99 |
| 45_I | 51_G | 1.374 | 0.99 |
| 7_G | 92_K | 1.363 | 0.99 |
| 78_Y | 97_V | 1.344 | 0.99 |
| 50_Y | 54_V | 1.335 | 0.99 |
| 13_Y | 106_K | 1.307 | 0.99 |
| 56_R | 95_A | 1.284 | 0.99 |
| 53_L | 99_L | 1.274 | 0.99 |
| 39_L | 78_Y | 1.263 | 0.99 |
| 62_V | 81_V | 1.258 | 0.99 |
| 62_V | 83_I | 1.250 | 0.99 |
| 26_D | 89_N | 1.244 | 0.98 |
| 32_N | 85_L | 1.238 | 0.98 |
| 54_V | 65_E | 1.228 | 0.98 |
| 73_T | 114_S | 1.196 | 0.98 |
| 51_G | 101_L | 1.184 | 0.98 |
| 9_I | 22_Y | 1.146 | 0.97 |
| 126_K | 131_T | 1.138 | 0.97 |
| 79_R | 128_F | 1.129 | 0.97 |
| 50_Y | 102_T | 1.106 | 0.96 |
| 43_V | 76_L | 1.103 | 0.96 |
| 43_V | 99_L | 1.088 | 0.96 |
| 5_V | 40_N | 1.087 | 0.96 |
| 49_Y | 101_L | 1.055 | 0.95 |
| 34_I | 81_V | 1.011 | 0.93 |
| 4_L | 42_R | 1.009 | 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
- 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 | |
| 3zf6A | 1 | 0.9697 | 100 | 0.115 | Contact Map |
| 3araA | 3 | 0.8636 | 100 | 0.117 | Contact Map |
| 3ca9A | 2 | 0.8561 | 100 | 0.126 | Contact Map |
| 4gv8A | 6 | 0.8788 | 100 | 0.127 | Contact Map |
| 3c2tA | 2 | 0.8561 | 100 | 0.137 | Contact Map |
| 3f4fA | 3 | 0.947 | 100 | 0.143 | Contact Map |
| 3ecyA | 2 | 0.8333 | 100 | 0.146 | Contact Map |
| 3hzaA | 1 | 0.9697 | 100 | 0.147 | Contact Map |
| 2p9oA | 3 | 0.8788 | 100 | 0.148 | Contact Map |
| 3p48A | 3 | 0.8712 | 100 | 0.159 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)