| cdomain 1-82 -force run |
| ID: | 1516681069 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (82) | ||
| Sequences: | 51 (31.5) | ||
| Seq/Len: | 0.622 | ||
| Nf(neff/√len): | 3.5 |
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: 0.622).
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 |
| 22_Y | 30_Y | 2.011 | 0.90 |
| 12_Y | 34_S | 1.784 | 0.81 |
| 12_Y | 25_S | 1.704 | 0.77 |
| 25_S | 34_S | 1.673 | 0.75 |
| 10_E | 71_I | 1.628 | 0.72 |
| 70_N | 76_P | 1.499 | 0.63 |
| 57_L | 61_E | 1.358 | 0.52 |
| 67_L | 78_A | 1.339 | 0.50 |
| 5_H | 20_L | 1.332 | 0.49 |
| 23_D | 36_N | 1.329 | 0.49 |
| 15_M | 18_K | 1.312 | 0.48 |
| 24_W | 74_V | 1.250 | 0.43 |
| 46_F | 53_S | 1.246 | 0.43 |
| 17_Q | 20_L | 1.242 | 0.42 |
| 3_I | 9_K | 1.233 | 0.41 |
| 6_S | 10_E | 1.202 | 0.39 |
| 17_Q | 44_D | 1.196 | 0.39 |
| 63_I | 81_L | 1.191 | 0.38 |
| 20_L | 30_Y | 1.173 | 0.37 |
| 23_D | 81_L | 1.165 | 0.36 |
| 41_E | 63_I | 1.124 | 0.33 |
| 60_N | 72_F | 1.122 | 0.33 |
| 70_N | 73_Q | 1.115 | 0.33 |
| 23_D | 45_E | 1.107 | 0.32 |
| 15_M | 75_S | 1.102 | 0.32 |
| 36_N | 45_E | 1.099 | 0.31 |
| 75_S | 78_A | 1.092 | 0.31 |
| 48_N | 52_Q | 1.081 | 0.30 |
| 43_Q | 62_S | 1.078 | 0.30 |
| 14_S | 31_F | 1.075 | 0.30 |
| 7_T | 12_Y | 1.068 | 0.29 |
| 18_K | 82_L | 1.067 | 0.29 |
| 43_Q | 82_L | 1.061 | 0.29 |
| 1_D | 55_P | 1.061 | 0.29 |
| 22_Y | 31_F | 1.056 | 0.28 |
| 24_W | 40_P | 1.048 | 0.28 |
| 5_H | 30_Y | 1.041 | 0.27 |
| 8_S | 81_L | 1.034 | 0.27 |
| 16_I | 36_N | 1.029 | 0.27 |
| 16_I | 23_D | 1.029 | 0.27 |
| 40_P | 74_V | 1.028 | 0.27 |
| 5_H | 22_Y | 1.024 | 0.26 |
| 26_T | 49_P | 1.024 | 0.26 |
| 54_S | 60_N | 1.016 | 0.26 |
| 14_S | 73_Q | 1.015 | 0.26 |
| 7_T | 24_W | 1.013 | 0.26 |
| 3_I | 6_S | 1.012 | 0.26 |
| 7_T | 74_V | 1.005 | 0.25 |
| 72_F | 75_S | 1.004 | 0.25 |
| 70_N | 80_M | 1.003 | 0.25 |
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 | |
| 4i9oA | 1 | 0.2561 | 44.4 | 0.912 | Contact Map |
| 2gutA | 1 | 0.4024 | 29.5 | 0.92 | Contact Map |
| 2k0nA | 1 | 0.439 | 23.9 | 0.923 | Contact Map |
| 2oniA | 1 | 0.9634 | 9.2 | 0.936 | Contact Map |
| 3olmA | 1 | 0.9634 | 6.7 | 0.94 | Contact Map |
| 1nd7A | 1 | 0.9634 | 5.9 | 0.942 | Contact Map |
| 1zvdA | 1 | 0.9634 | 5.8 | 0.942 | Contact Map |
| 1sumB | 1 | 0.4146 | 4.1 | 0.946 | Contact Map |
| 2g40A | 1 | 0.378 | 4.1 | 0.946 | Contact Map |
| 4dr0A | 2 | 0.6829 | 4 | 0.946 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)