| PLS 2 N Term |
| ID: | 1474310324 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 72 (68) | ||
| Sequences: | 20868 (13099.2) | ||
| Seq/Len: | 306.882 | ||
| Nf(neff/√len): | 1588.5 |
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: 306.882).
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 |
| 28_Y | 68_R | 4.312 | 1.00 |
| 15_R | 71_F | 2.663 | 1.00 |
| 21_V | 37_L | 2.478 | 1.00 |
| 26_N | 33_E | 2.248 | 1.00 |
| 15_R | 19_A | 1.950 | 1.00 |
| 62_D | 65_Q | 1.877 | 1.00 |
| 19_A | 25_G | 1.807 | 1.00 |
| 62_D | 67_G | 1.711 | 1.00 |
| 35_N | 47_G | 1.711 | 1.00 |
| 22_D | 27_G | 1.679 | 1.00 |
| 62_D | 66_D | 1.664 | 1.00 |
| 31_F | 51_R | 1.647 | 1.00 |
| 22_D | 25_G | 1.627 | 1.00 |
| 28_Y | 70_S | 1.623 | 1.00 |
| 23_T | 36_D | 1.622 | 1.00 |
| 66_D | 70_S | 1.613 | 1.00 |
| 7_S | 10_E | 1.418 | 1.00 |
| 17_A | 21_V | 1.392 | 0.99 |
| 22_D | 26_N | 1.369 | 0.99 |
| 46_P | 49_R | 1.342 | 0.99 |
| 20_K | 40_A | 1.279 | 0.99 |
| 26_N | 30_S | 1.253 | 0.99 |
| 24_D | 33_E | 1.246 | 0.98 |
| 30_S | 33_E | 1.245 | 0.98 |
| 64_D | 70_S | 1.237 | 0.98 |
| 11_M | 15_R | 1.207 | 0.98 |
| 6_V | 10_E | 1.194 | 0.98 |
| 19_A | 71_F | 1.138 | 0.97 |
| 13_E | 16_E | 1.131 | 0.97 |
| 23_T | 33_E | 1.129 | 0.97 |
| 31_F | 55_E | 1.071 | 0.95 |
| 16_E | 20_K | 1.049 | 0.94 |
| 34_L | 58_M | 1.037 | 0.94 |
| 17_A | 20_K | 1.022 | 0.93 |
| 22_D | 33_E | 1.018 | 0.93 |
| 31_F | 54_T | 1.000 | 0.92 |
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 | |
| 4il1A | 4 | 0 | 97.9 | 0.056 | Contact Map |
| 2lc5A | 1 | 0.9444 | 97.8 | 0.078 | Contact Map |
| 3ox6A | 6 | 0.9306 | 97.8 | 0.081 | Contact Map |
| 4d1eA | 1 | 0.9444 | 97.8 | 0.082 | Contact Map |
| 2f33A | 1 | 0.9306 | 97.8 | 0.085 | Contact Map |
| 4mvfA | 1 | 0.9444 | 97.7 | 0.088 | Contact Map |
| 1s6iA | 1 | 0.9167 | 97.6 | 0.105 | Contact Map |
| 4gjfA | 1 | 0.9028 | 97.6 | 0.106 | Contact Map |
| 2jjzA | 1 | 0.9444 | 97.6 | 0.109 | Contact Map |
| 3pm8A | 2 | 0.8889 | 97.6 | 0.112 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)