| Ysf3 |
| ID: | 1490545922 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 85 (83) | ||
| Sequences: | 273 (153.2) | ||
| Seq/Len: | 3.289 | ||
| Nf(neff/√len): | 16.8 |
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: 3.289).
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 |
| 39_T | 43_L | 2.910 | 1.00 |
| 10_L | 14_Y | 2.185 | 1.00 |
| 39_T | 53_V | 1.798 | 0.99 |
| 60_L | 63_R | 1.776 | 0.99 |
| 42_T | 46_H | 1.596 | 0.98 |
| 81_L | 84_E | 1.516 | 0.97 |
| 5_Q | 8_L | 1.484 | 0.96 |
| 26_T | 50_L | 1.475 | 0.96 |
| 32_Q | 35_V | 1.440 | 0.95 |
| 77_Y | 80_Y | 1.423 | 0.95 |
| 3_E | 26_T | 1.410 | 0.94 |
| 75_P | 79_A | 1.405 | 0.94 |
| 76_G | 80_Y | 1.393 | 0.94 |
| 47_S | 69_L | 1.376 | 0.93 |
| 10_L | 13_I | 1.356 | 0.93 |
| 43_L | 53_V | 1.343 | 0.92 |
| 54_S | 65_T | 1.337 | 0.92 |
| 28_R | 35_V | 1.337 | 0.92 |
| 43_L | 49_S | 1.287 | 0.90 |
| 65_T | 69_L | 1.232 | 0.87 |
| 17_K | 20_G | 1.231 | 0.87 |
| 6_R | 9_K | 1.222 | 0.87 |
| 11_Q | 23_D | 1.212 | 0.86 |
| 15_K | 34_N | 1.203 | 0.85 |
| 76_G | 79_A | 1.183 | 0.84 |
| 3_E | 6_R | 1.175 | 0.83 |
| 26_T | 62_I | 1.160 | 0.82 |
| 62_I | 67_I | 1.147 | 0.81 |
| 29_E | 33_R | 1.126 | 0.80 |
| 7_Q | 13_I | 1.119 | 0.79 |
| 27_T | 50_L | 1.110 | 0.78 |
| 47_S | 58_G | 1.104 | 0.78 |
| 57_R | 68_H | 1.095 | 0.77 |
| 1_M | 4_K | 1.094 | 0.77 |
| 40_L | 56_S | 1.092 | 0.77 |
| 55_L | 69_L | 1.091 | 0.77 |
| 40_L | 44_Q | 1.090 | 0.77 |
| 46_H | 66_R | 1.087 | 0.76 |
| 20_G | 38_D | 1.081 | 0.76 |
| 17_K | 58_G | 1.073 | 0.75 |
| 2_A | 62_I | 1.061 | 0.74 |
| 4_K | 77_Y | 1.054 | 0.73 |
| 2_A | 15_K | 1.038 | 0.72 |
| 11_Q | 15_K | 1.027 | 0.70 |
| 50_L | 66_R | 1.020 | 0.70 |
| 17_K | 69_L | 1.017 | 0.69 |
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 | |
| 1jqnA | 1 | 0.8353 | 4.6 | 0.933 | Contact Map |
| 3fxdA | 2 | 0.5176 | 2.8 | 0.94 | Contact Map |
| 2q88A | 1 | 0.4 | 2.8 | 0.94 | Contact Map |
| 4lt5A | 1 | 0.8941 | 2.7 | 0.94 | Contact Map |
| 4bxhA | 1 | 0.8235 | 2.7 | 0.941 | Contact Map |
| 4nfnA | 1 | 0.4118 | 2.3 | 0.942 | Contact Map |
| 2izrA | 1 | 0.4706 | 2.1 | 0.944 | Contact Map |
| 4twcA | 2 | 0.4235 | 1.8 | 0.946 | Contact Map |
| 2azeC | 1 | 0.4118 | 1.8 | 0.946 | Contact Map |
| 2k85A | 1 | 0.6706 | 1.7 | 0.947 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)