| prolactin cut filtered |
| ID: | 1465288779 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 55 (55) | ||
| Sequences: | 593 (451.1) | ||
| Seq/Len: | 10.782 | ||
| Nf(neff/√len): | 60.8 |
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: 10.782).
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 |
| 52_V | 55_P | 2.253 | 1.00 |
| 46_T | 55_P | 1.957 | 1.00 |
| 51_P | 54_G | 1.941 | 1.00 |
| 49_F | 54_G | 1.660 | 1.00 |
| 9_S | 36_A | 1.503 | 1.00 |
| 22_V | 26_S | 1.434 | 1.00 |
| 7_I | 49_F | 1.421 | 1.00 |
| 19_W | 22_V | 1.386 | 0.99 |
| 15_D | 29_I | 1.375 | 0.99 |
| 40_K | 46_T | 1.352 | 0.99 |
| 5_I | 51_P | 1.254 | 0.99 |
| 2_A | 42_Y | 1.240 | 0.98 |
| 20_I | 23_A | 1.237 | 0.98 |
| 43_S | 54_G | 1.218 | 0.98 |
| 23_A | 34_V | 1.207 | 0.98 |
| 48_I | 51_P | 1.179 | 0.98 |
| 11_F | 20_I | 1.174 | 0.98 |
| 43_S | 47_C | 1.151 | 0.97 |
| 5_I | 49_F | 1.143 | 0.97 |
| 44_M | 50_P | 1.136 | 0.97 |
| 5_I | 8_P | 1.122 | 0.97 |
| 42_Y | 45_V | 1.119 | 0.96 |
| 17_T | 36_A | 1.085 | 0.96 |
| 18_V | 28_V | 1.081 | 0.95 |
| 1_P | 25_L | 1.073 | 0.95 |
| 8_P | 28_V | 1.061 | 0.95 |
| 25_L | 30_C | 1.054 | 0.95 |
| 37_V | 52_V | 1.049 | 0.94 |
| 29_I | 35_W | 1.038 | 0.94 |
| 18_V | 32_I | 1.034 | 0.94 |
| 21_S | 28_V | 1.006 | 0.93 |
| 18_V | 22_V | 1.004 | 0.93 |
| 10_D | 13_M | 1.002 | 0.92 |
| 35_W | 43_S | 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 | |
| 2mv6A | 1 | 0.8545 | 82.3 | 0.516 | Contact Map |
| 3lb6C | 1 | 0.0364 | 43.7 | 0.629 | Contact Map |
| 1q55A | 4 | 0.1455 | 14.4 | 0.707 | Contact Map |
| 2k9yA | 2 | 0.7273 | 12.4 | 0.717 | Contact Map |
| 3j8f7 | 1 | 0.1636 | 6.4 | 0.751 | Contact Map |
| 2jwaA | 2 | 0.7455 | 6.3 | 0.751 | Contact Map |
| 3j6da | 24 | 0 | 3.9 | 0.775 | Contact Map |
| 4ev6A | 5 | 0.7818 | 3.3 | 0.782 | Contact Map |
| 4i0uA | 10 | 0.7455 | 3.3 | 0.783 | Contact Map |
| 1cd1A | 2 | 0.0909 | 2.8 | 0.791 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)