| leafs_1ptf_fastRelax_16 |
| ID: | 1507536333 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 470 (260.2) | ||
| Seq/Len: | 5.402 | ||
| Nf(neff/√len): | 27.9 |
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: 5.402).
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 |
| 6_L | 78_V | 3.042 | 1.00 |
| 25_S | 80_T | 2.821 | 1.00 |
| 1_G | 66_Y | 2.673 | 1.00 |
| 44_F | 81_F | 2.314 | 1.00 |
| 33_F | 63_L | 2.111 | 1.00 |
| 2_L | 71_D | 1.954 | 1.00 |
| 20_V | 47_W | 1.845 | 1.00 |
| 32_L | 41_W | 1.734 | 1.00 |
| 5_L | 49_L | 1.686 | 1.00 |
| 28_L | 37_R | 1.660 | 1.00 |
| 35_L | 44_F | 1.609 | 0.99 |
| 24_V | 47_W | 1.560 | 0.99 |
| 15_I | 24_V | 1.545 | 0.99 |
| 23_Q | 27_N | 1.499 | 0.99 |
| 36_I | 41_W | 1.481 | 0.99 |
| 7_L | 60_L | 1.430 | 0.98 |
| 23_Q | 38_N | 1.402 | 0.98 |
| 34_V | 41_W | 1.397 | 0.98 |
| 36_I | 55_P | 1.347 | 0.97 |
| 37_R | 55_P | 1.332 | 0.97 |
| 34_V | 44_F | 1.330 | 0.97 |
| 42_R | 82_R | 1.309 | 0.96 |
| 17_S | 51_H | 1.215 | 0.94 |
| 15_I | 56_R | 1.152 | 0.91 |
| 4_R | 78_V | 1.114 | 0.89 |
| 9_L | 85_R | 1.098 | 0.88 |
| 11_P | 78_V | 1.098 | 0.88 |
| 10_D | 39_L | 1.091 | 0.88 |
| 20_V | 84_L | 1.088 | 0.88 |
| 81_F | 86_I | 1.070 | 0.87 |
| 44_F | 63_L | 1.068 | 0.86 |
| 36_I | 57_R | 1.065 | 0.86 |
| 52_S | 70_E | 1.059 | 0.86 |
| 1_G | 21_M | 1.058 | 0.86 |
| 75_R | 78_V | 1.036 | 0.84 |
| 42_R | 53_L | 1.030 | 0.84 |
| 37_R | 52_S | 1.030 | 0.84 |
| 7_L | 64_Y | 1.026 | 0.83 |
| 8_I | 27_N | 1.008 | 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 | |
| 1kklH | 3 | 1 | 95.5 | 0.836 | Contact Map |
| 1ka5A | 1 | 1 | 95.5 | 0.836 | Contact Map |
| 3ccdA | 2 | 0.977 | 95.3 | 0.838 | Contact Map |
| 3ihsA | 2 | 0.9425 | 95.2 | 0.839 | Contact Map |
| 1ptfA | 1 | 1 | 95.1 | 0.84 | Contact Map |
| 1pchA | 1 | 0.9885 | 94.7 | 0.844 | Contact Map |
| 1y51A | 3 | 0.9885 | 94.5 | 0.845 | Contact Map |
| 1sphA | 2 | 0.9885 | 94.4 | 0.846 | Contact Map |
| 3le1A | 2 | 0.9885 | 93.5 | 0.852 | Contact Map |
| 3pqaA | 4 | 0.5057 | 8.5 | 0.934 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)