| wwox 16-91 |
| ID: | 1494761054 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 76 (74) | ||
| Sequences: | 1599 (1051.2) | ||
| Seq/Len: | 21.608 | ||
| Nf(neff/√len): | 122.2 |
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: 21.608).
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 |
| 3_L | 6_G | 2.135 | 1.00 |
| 52_T | 58_V | 2.084 | 1.00 |
| 11_T | 17_V | 2.070 | 1.00 |
| 44_L | 47_G | 2.061 | 1.00 |
| 62_D | 65_N | 2.044 | 1.00 |
| 47_G | 64_I | 1.959 | 1.00 |
| 21_N | 28_Q | 1.899 | 1.00 |
| 9_E | 17_V | 1.893 | 1.00 |
| 8_E | 22_H | 1.777 | 1.00 |
| 50_Q | 58_V | 1.750 | 1.00 |
| 49_E | 63_H | 1.730 | 1.00 |
| 6_G | 23_T | 1.534 | 1.00 |
| 7_W | 19_Y | 1.448 | 1.00 |
| 10_R | 20_A | 1.447 | 1.00 |
| 51_E | 57_Q | 1.396 | 0.99 |
| 51_E | 61_V | 1.340 | 0.99 |
| 18_Y | 29_W | 1.327 | 0.99 |
| 52_T | 56_G | 1.312 | 0.99 |
| 45_P | 48_W | 1.267 | 0.99 |
| 37_R | 40_V | 1.215 | 0.98 |
| 16_W | 57_Q | 1.214 | 0.98 |
| 21_N | 24_E | 1.176 | 0.98 |
| 60_F | 72_D | 1.176 | 0.98 |
| 14_D | 30_E | 1.172 | 0.98 |
| 12_T | 16_W | 1.154 | 0.97 |
| 53_D | 59_F | 1.150 | 0.97 |
| 20_A | 27_T | 1.148 | 0.97 |
| 59_F | 70_Y | 1.129 | 0.97 |
| 63_H | 68_T | 1.094 | 0.96 |
| 19_Y | 31_H | 1.054 | 0.95 |
| 70_Y | 73_P | 1.050 | 0.94 |
| 27_T | 32_P | 1.047 | 0.94 |
| 21_N | 26_K | 1.047 | 0.94 |
| 29_W | 32_P | 1.045 | 0.94 |
| 10_R | 51_E | 1.042 | 0.94 |
| 2_E | 43_D | 1.029 | 0.94 |
| 63_H | 66_K | 1.028 | 0.94 |
| 69_T | 73_P | 1.012 | 0.93 |
| 53_D | 57_Q | 1.004 | 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 | |
| 2kxqA | 1 | 1 | 99.7 | 0.07 | Contact Map |
| 1tk7A | 1 | 0.9868 | 99.7 | 0.074 | Contact Map |
| 4rohA | 1 | 0.9342 | 99.7 | 0.079 | Contact Map |
| 2l5fA | 1 | 1 | 99.7 | 0.101 | Contact Map |
| 2jxwA | 1 | 0.9868 | 99.7 | 0.123 | Contact Map |
| 1o6wA | 1 | 0.9605 | 99.6 | 0.171 | Contact Map |
| 3l4hA | 1 | 0.8158 | 99.2 | 0.314 | Contact Map |
| 2dwvA | 2 | 0.6053 | 98.7 | 0.439 | Contact Map |
| 1eg3A | 1 | 0.5658 | 98.6 | 0.457 | Contact Map |
| 2ysdA | 1 | 0.5921 | 98.6 | 0.463 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)