| T0808 330-418 -force run |
| ID: | 1405035089 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (87) | ||
| Sequences: | 84 (72.7) | ||
| Seq/Len: | 0.966 | ||
| Nf(neff/√len): | 7.8 |
Jackhmmer Results: (2014_04_16)
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: 0.966).
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 |
| 34_A | 42_Y | 2.092 | 0.97 |
| 24_T | 72_C | 2.080 | 0.96 |
| 33_T | 70_F | 1.715 | 0.87 |
| 22_R | 72_C | 1.691 | 0.86 |
| 13_A | 77_K | 1.604 | 0.82 |
| 5_E | 48_K | 1.583 | 0.81 |
| 30_H | 66_M | 1.572 | 0.80 |
| 8_F | 63_S | 1.548 | 0.79 |
| 56_M | 60_F | 1.481 | 0.74 |
| 44_G | 56_M | 1.476 | 0.74 |
| 44_G | 60_F | 1.428 | 0.71 |
| 8_F | 32_A | 1.424 | 0.70 |
| 2_L | 53_Y | 1.413 | 0.69 |
| 29_T | 34_A | 1.387 | 0.67 |
| 8_F | 54_L | 1.364 | 0.65 |
| 11_Q | 26_A | 1.319 | 0.62 |
| 30_H | 34_A | 1.298 | 0.60 |
| 33_T | 59_F | 1.293 | 0.59 |
| 41_D | 59_F | 1.288 | 0.59 |
| 33_T | 36_A | 1.274 | 0.58 |
| 33_T | 44_G | 1.256 | 0.56 |
| 36_A | 57_G | 1.252 | 0.56 |
| 11_Q | 59_F | 1.233 | 0.54 |
| 25_D | 71_Y | 1.232 | 0.54 |
| 13_A | 64_V | 1.228 | 0.54 |
| 3_S | 55_K | 1.225 | 0.53 |
| 24_T | 76_G | 1.219 | 0.53 |
| 8_F | 27_T | 1.201 | 0.51 |
| 53_Y | 66_M | 1.184 | 0.49 |
| 44_G | 59_F | 1.171 | 0.48 |
| 33_T | 56_M | 1.144 | 0.46 |
| 12_W | 20_W | 1.132 | 0.45 |
| 31_D | 44_G | 1.126 | 0.44 |
| 31_D | 54_L | 1.124 | 0.44 |
| 12_W | 79_P | 1.121 | 0.44 |
| 16_K | 28_F | 1.109 | 0.43 |
| 14_R | 78_E | 1.100 | 0.42 |
| 74_P | 77_K | 1.090 | 0.41 |
| 6_V | 80_E | 1.084 | 0.40 |
| 34_A | 60_F | 1.077 | 0.40 |
| 81_I | 86_L | 1.073 | 0.39 |
| 15_S | 21_S | 1.050 | 0.37 |
| 33_T | 57_G | 1.042 | 0.37 |
| 30_H | 43_Q | 1.042 | 0.37 |
| 77_K | 82_D | 1.036 | 0.36 |
| 64_V | 73_K | 1.014 | 0.34 |
| 12_W | 24_T | 1.013 | 0.34 |
| 25_D | 81_I | 1.012 | 0.34 |
| 45_G | 53_Y | 1.011 | 0.34 |
| 82_D | 85_A | 1.007 | 0.34 |
| 59_F | 70_F | 1.003 | 0.33 |
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 | |
| 4h2gA | 1 | 0.8876 | 10.6 | 0.929 | Contact Map |
| 3owtC | 1 | 0.1236 | 8.4 | 0.932 | Contact Map |
| 3zyqA | 1 | 0.2921 | 6.9 | 0.935 | Contact Map |
| 4h62V | 1 | 0.0899 | 5.6 | 0.937 | Contact Map |
| 2llzA | 1 | 0.7079 | 5.3 | 0.938 | Contact Map |
| 3ztvA | 1 | 0.9551 | 4.9 | 0.939 | Contact Map |
| 3cskA | 1 | 0.764 | 4.2 | 0.941 | Contact Map |
| 2bsgA | 3 | 0.3034 | 3.9 | 0.942 | Contact Map |
| 1ojjA | 2 | 0.8202 | 3.6 | 0.943 | Contact Map |
| 2ovwA | 4 | 0.8202 | 3.6 | 0.943 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)