| leafs_1ptf_fastRelax_31 |
| ID: | 1507536452 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 467 (232.4) | ||
| Seq/Len: | 5.368 | ||
| Nf(neff/√len): | 24.9 |
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: 5.368).
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 |
| 38_N | 59_Q | 5.950 | 1.00 |
| 16_D | 20_R | 4.319 | 1.00 |
| 29_F | 76_T | 3.139 | 1.00 |
| 42_I | 64_V | 2.573 | 1.00 |
| 10_A | 18_Y | 2.058 | 1.00 |
| 7_I | 60_T | 1.727 | 1.00 |
| 25_D | 80_I | 1.688 | 1.00 |
| 64_V | 80_I | 1.666 | 1.00 |
| 14_I | 50_I | 1.625 | 0.99 |
| 2_A | 71_W | 1.599 | 0.99 |
| 3_V | 62_I | 1.588 | 0.99 |
| 2_A | 74_F | 1.471 | 0.98 |
| 25_D | 28_R | 1.392 | 0.98 |
| 41_R | 64_V | 1.314 | 0.96 |
| 4_L | 38_N | 1.219 | 0.94 |
| 48_E | 52_N | 1.215 | 0.94 |
| 21_I | 84_H | 1.190 | 0.93 |
| 6_I | 77_L | 1.158 | 0.91 |
| 12_D | 16_D | 1.153 | 0.91 |
| 50_I | 64_V | 1.141 | 0.91 |
| 30_K | 68_K | 1.132 | 0.90 |
| 26_A | 29_F | 1.121 | 0.90 |
| 78_L | 82_R | 1.102 | 0.88 |
| 9_I | 16_D | 1.101 | 0.88 |
| 3_V | 56_P | 1.099 | 0.88 |
| 15_R | 40_S | 1.090 | 0.88 |
| 20_R | 50_I | 1.051 | 0.85 |
| 12_D | 68_K | 1.045 | 0.85 |
| 38_N | 42_I | 1.045 | 0.85 |
| 56_P | 68_K | 1.043 | 0.84 |
| 7_I | 85_R | 1.042 | 0.84 |
| 3_V | 51_H | 1.024 | 0.83 |
| 68_K | 78_L | 1.020 | 0.83 |
| 12_D | 51_H | 1.015 | 0.82 |
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 | 93.1 | 0.868 | Contact Map |
| 1pchA | 1 | 0.9885 | 93 | 0.868 | Contact Map |
| 1ka5A | 1 | 1 | 93 | 0.869 | Contact Map |
| 1kklH | 3 | 1 | 92.9 | 0.869 | Contact Map |
| 1ptfA | 1 | 1 | 91.8 | 0.873 | Contact Map |
| 3ihsA | 2 | 0.9425 | 91.8 | 0.873 | Contact Map |
| 1y51A | 3 | 0.9885 | 91 | 0.876 | Contact Map |
| 1sphA | 2 | 0.9885 | 90.8 | 0.876 | Contact Map |
| 3le1A | 2 | 0.9885 | 87.2 | 0.884 | Contact Map |
| 4wlrA | 1 | 0.5977 | 4.7 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)