| leafs_1ptf_fastRelax_1 |
| ID: | 1507536175 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 493 (337.1) | ||
| Seq/Len: | 5.667 | ||
| Nf(neff/√len): | 36.1 |
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: 5.667).
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 |
| 4_Y | 78_L | 2.448 | 1.00 |
| 79_E | 83_F | 2.308 | 1.00 |
| 22_L | 25_L | 2.095 | 1.00 |
| 36_L | 41_I | 2.009 | 1.00 |
| 38_R | 60_E | 1.839 | 1.00 |
| 72_D | 75_R | 1.810 | 1.00 |
| 48_E | 63_I | 1.759 | 1.00 |
| 34_W | 43_L | 1.713 | 1.00 |
| 55_V | 71_R | 1.655 | 1.00 |
| 8_V | 15_D | 1.604 | 0.99 |
| 27_D | 32_P | 1.543 | 0.99 |
| 35_L | 42_I | 1.539 | 0.99 |
| 10_E | 58_D | 1.454 | 0.99 |
| 5_W | 62_L | 1.446 | 0.98 |
| 56_D | 86_L | 1.424 | 0.98 |
| 65_V | 74_L | 1.405 | 0.98 |
| 3_F | 48_E | 1.402 | 0.98 |
| 37_Y | 58_D | 1.400 | 0.98 |
| 2_L | 84_E | 1.346 | 0.97 |
| 32_P | 39_G | 1.321 | 0.97 |
| 10_E | 51_R | 1.302 | 0.96 |
| 15_D | 54_D | 1.271 | 0.96 |
| 42_I | 75_R | 1.241 | 0.95 |
| 10_E | 56_D | 1.213 | 0.94 |
| 37_Y | 59_I | 1.209 | 0.94 |
| 20_I | 24_R | 1.205 | 0.94 |
| 1_D | 66_T | 1.172 | 0.93 |
| 50_L | 53_L | 1.154 | 0.92 |
| 33_L | 54_D | 1.118 | 0.90 |
| 17_R | 35_L | 1.104 | 0.89 |
| 19_A | 74_L | 1.100 | 0.89 |
| 33_L | 74_L | 1.084 | 0.88 |
| 21_A | 79_E | 1.062 | 0.87 |
| 29_F | 63_I | 1.062 | 0.87 |
| 24_R | 64_V | 1.061 | 0.87 |
| 81_L | 85_R | 1.050 | 0.86 |
| 7_V | 23_I | 1.049 | 0.86 |
| 4_Y | 48_E | 1.046 | 0.86 |
| 17_R | 60_E | 1.043 | 0.86 |
| 17_R | 45_L | 1.042 | 0.85 |
| 38_R | 52_R | 1.037 | 0.85 |
| 70_A | 74_L | 1.034 | 0.85 |
| 21_A | 77_T | 1.027 | 0.84 |
| 62_L | 70_A | 1.020 | 0.84 |
| 46_V | 66_T | 1.010 | 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
- 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 | |
| 1ka5A | 1 | 1 | 98 | 0.761 | Contact Map |
| 1kklH | 3 | 1 | 98 | 0.763 | Contact Map |
| 1ptfA | 1 | 1 | 97.9 | 0.764 | Contact Map |
| 1sphA | 2 | 0.9885 | 97.9 | 0.767 | Contact Map |
| 1y51A | 3 | 0.9885 | 97.9 | 0.769 | Contact Map |
| 1pchA | 1 | 0.9885 | 97.8 | 0.77 | Contact Map |
| 3ccdA | 2 | 0.977 | 97.8 | 0.773 | Contact Map |
| 3ihsA | 2 | 0.8966 | 97.7 | 0.775 | Contact Map |
| 3le1A | 2 | 0.9885 | 97.6 | 0.783 | Contact Map |
| 1vhfA | 1 | 0.3218 | 5.7 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)