| leafs_1ptf_fastRelax_10 |
| ID: | 1507536266 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 501 (372.4) | ||
| Seq/Len: | 5.759 | ||
| Nf(neff/√len): | 39.9 |
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: 5.759).
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 |
| 11_E | 17_H | 3.014 | 1.00 |
| 35_L | 42_I | 2.528 | 1.00 |
| 4_E | 74_F | 2.364 | 1.00 |
| 30_D | 68_S | 2.170 | 1.00 |
| 20_I | 47_W | 2.153 | 1.00 |
| 49_M | 52_A | 1.853 | 1.00 |
| 5_I | 62_K | 1.738 | 1.00 |
| 74_F | 78_L | 1.719 | 1.00 |
| 21_I | 84_A | 1.602 | 0.99 |
| 8_V | 81_L | 1.589 | 0.99 |
| 7_I | 60_E | 1.579 | 0.99 |
| 10_A | 33_F | 1.514 | 0.99 |
| 3_A | 74_F | 1.508 | 0.99 |
| 45_R | 80_L | 1.501 | 0.99 |
| 26_A | 42_I | 1.471 | 0.99 |
| 14_L | 50_I | 1.458 | 0.99 |
| 4_E | 78_L | 1.365 | 0.98 |
| 9_R | 85_N | 1.308 | 0.97 |
| 2_I | 63_I | 1.295 | 0.96 |
| 27_T | 72_S | 1.292 | 0.96 |
| 26_A | 33_F | 1.271 | 0.96 |
| 4_E | 50_I | 1.259 | 0.96 |
| 11_E | 63_I | 1.257 | 0.96 |
| 18_I | 50_I | 1.238 | 0.95 |
| 2_I | 74_F | 1.219 | 0.95 |
| 35_L | 50_I | 1.163 | 0.93 |
| 32_Q | 81_L | 1.160 | 0.92 |
| 10_A | 29_F | 1.153 | 0.92 |
| 37_G | 45_R | 1.148 | 0.92 |
| 18_I | 68_S | 1.142 | 0.92 |
| 46_K | 49_M | 1.129 | 0.91 |
| 18_I | 30_D | 1.120 | 0.91 |
| 24_E | 72_S | 1.119 | 0.91 |
| 30_D | 34_I | 1.108 | 0.90 |
| 7_I | 50_I | 1.106 | 0.90 |
| 12_V | 17_H | 1.096 | 0.89 |
| 1_P | 86_I | 1.092 | 0.89 |
| 34_I | 82_L | 1.085 | 0.89 |
| 80_L | 86_I | 1.043 | 0.86 |
| 10_A | 18_I | 1.035 | 0.85 |
| 23_H | 27_T | 1.035 | 0.85 |
| 18_I | 62_K | 1.021 | 0.84 |
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 | |
| 3ccdA | 2 | 0.977 | 89.1 | 0.857 | Contact Map |
| 1kklH | 3 | 1 | 87.2 | 0.861 | Contact Map |
| 1ka5A | 1 | 1 | 86.7 | 0.862 | Contact Map |
| 1ptfA | 1 | 1 | 86 | 0.864 | Contact Map |
| 3ihsA | 2 | 0.9425 | 84.4 | 0.867 | Contact Map |
| 1pchA | 1 | 0.9885 | 82.3 | 0.87 | Contact Map |
| 1sphA | 2 | 0.9885 | 81.4 | 0.871 | Contact Map |
| 1y51A | 3 | 0.9885 | 81 | 0.871 | Contact Map |
| 3le1A | 2 | 0.9885 | 74.8 | 0.878 | Contact Map |
| 2k2wA | 1 | 0.3333 | 2.2 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)