| leafs_1ptf_fastRelax_7 |
| ID: | 1507536227 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 505 (377.6) | ||
| Seq/Len: | 5.805 | ||
| Nf(neff/√len): | 40.5 |
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: 5.805).
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 |
| 30_R | 68_D | 3.218 | 1.00 |
| 44_I | 77_V | 2.241 | 1.00 |
| 2_A | 71_R | 2.194 | 1.00 |
| 38_D | 56_Y | 2.045 | 1.00 |
| 79_I | 83_S | 1.842 | 1.00 |
| 25_L | 83_S | 1.740 | 1.00 |
| 34_L | 77_V | 1.729 | 1.00 |
| 7_V | 60_V | 1.628 | 0.99 |
| 14_P | 66_F | 1.602 | 0.99 |
| 8_V | 80_A | 1.571 | 0.99 |
| 44_I | 61_L | 1.547 | 0.99 |
| 10_L | 18_F | 1.539 | 0.99 |
| 33_F | 70_A | 1.517 | 0.99 |
| 21_I | 47_W | 1.457 | 0.99 |
| 40_Y | 54_P | 1.437 | 0.98 |
| 20_A | 47_W | 1.375 | 0.98 |
| 4_D | 21_I | 1.367 | 0.98 |
| 54_P | 62_L | 1.357 | 0.98 |
| 46_I | 49_D | 1.332 | 0.97 |
| 14_P | 85_L | 1.241 | 0.95 |
| 7_V | 53_F | 1.217 | 0.95 |
| 36_H | 40_Y | 1.210 | 0.94 |
| 4_D | 78_R | 1.187 | 0.94 |
| 33_F | 83_S | 1.181 | 0.93 |
| 46_I | 84_H | 1.164 | 0.93 |
| 25_L | 39_S | 1.161 | 0.93 |
| 33_F | 40_Y | 1.145 | 0.92 |
| 6_F | 24_R | 1.130 | 0.91 |
| 70_A | 82_L | 1.113 | 0.90 |
| 29_H | 83_S | 1.097 | 0.89 |
| 18_F | 83_S | 1.088 | 0.89 |
| 25_L | 84_H | 1.086 | 0.89 |
| 46_I | 82_L | 1.058 | 0.87 |
| 14_P | 84_H | 1.047 | 0.86 |
| 11_L | 48_L | 1.038 | 0.86 |
| 78_R | 82_L | 1.031 | 0.85 |
| 29_H | 81_F | 1.029 | 0.85 |
| 25_L | 28_L | 1.029 | 0.85 |
| 3_L | 23_A | 1.026 | 0.85 |
| 42_I | 71_R | 1.024 | 0.85 |
| 25_L | 36_H | 1.018 | 0.84 |
| 60_V | 78_R | 1.009 | 0.83 |
| 15_L | 29_H | 1.003 | 0.83 |
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 | |
| 1pchA | 1 | 0.9885 | 70.9 | 0.886 | Contact Map |
| 1kklH | 3 | 1 | 70.9 | 0.886 | Contact Map |
| 1ka5A | 1 | 1 | 63.4 | 0.892 | Contact Map |
| 1ptfA | 1 | 1 | 62 | 0.893 | Contact Map |
| 1sphA | 2 | 0.9885 | 57.3 | 0.896 | Contact Map |
| 3ccdA | 2 | 0.977 | 56.9 | 0.896 | Contact Map |
| 1y51A | 3 | 0.9885 | 55.7 | 0.897 | Contact Map |
| 3ihsA | 2 | 0.908 | 49.4 | 0.9 | Contact Map |
| 3le1A | 2 | 0.9885 | 42.1 | 0.904 | Contact Map |
| 2q8nA | 3 | 0.977 | 2.3 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)