| prolactin cut manually |
| ID: | 1465210617 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (56) | ||
| Sequences: | 948 (621.6) | ||
| Seq/Len: | 16.929 | ||
| Nf(neff/√len): | 83.1 |
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: 16.929).
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 |
| 53_V | 56_P | 2.509 | 1.00 |
| 23_V | 27_S | 1.800 | 1.00 |
| 44_S | 55_G | 1.783 | 1.00 |
| 50_F | 53_V | 1.688 | 1.00 |
| 6_I | 52_P | 1.684 | 1.00 |
| 8_I | 50_F | 1.604 | 1.00 |
| 52_P | 55_G | 1.579 | 1.00 |
| 41_K | 47_T | 1.531 | 1.00 |
| 20_W | 23_V | 1.434 | 1.00 |
| 19_V | 29_V | 1.421 | 1.00 |
| 6_I | 9_P | 1.409 | 1.00 |
| 10_S | 37_A | 1.351 | 0.99 |
| 30_I | 36_W | 1.320 | 0.99 |
| 6_I | 50_F | 1.186 | 0.98 |
| 47_T | 56_P | 1.167 | 0.97 |
| 50_F | 55_G | 1.150 | 0.97 |
| 46_V | 52_P | 1.136 | 0.97 |
| 33_I | 36_W | 1.124 | 0.97 |
| 43_Y | 47_T | 1.123 | 0.97 |
| 11_D | 14_M | 1.119 | 0.96 |
| 3_A | 6_I | 1.112 | 0.96 |
| 49_I | 52_P | 1.101 | 0.96 |
| 5_F | 55_G | 1.088 | 0.96 |
| 45_M | 51_P | 1.085 | 0.96 |
| 16_D | 30_I | 1.074 | 0.95 |
| 43_Y | 46_V | 1.069 | 0.95 |
| 13_T | 17_T | 1.067 | 0.95 |
| 44_S | 48_C | 1.067 | 0.95 |
| 19_V | 33_I | 1.013 | 0.93 |
| 12_F | 21_I | 1.000 | 0.92 |
| 25_V | 40_L | 1.000 | 0.92 |
| 28_A | 38_V | 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 | 0.8571 | 65.1 | 0.532 | Contact Map |
| 3lb6C | 1 | 0.0536 | 40.3 | 0.596 | Contact Map |
| 1bquA | 2 | 0.3571 | 11.3 | 0.69 | Contact Map |
| 3besR | 1 | 0.7857 | 11.3 | 0.69 | Contact Map |
| 4jzjC | 2 | 0.1071 | 8.8 | 0.705 | Contact Map |
| 1q55A | 4 | 0.1607 | 6.3 | 0.725 | Contact Map |
| 3j8f7 | 1 | 0.1786 | 5.2 | 0.735 | Contact Map |
| 2k9yA | 2 | 0.7143 | 5 | 0.737 | Contact Map |
| 1zrtD | 2 | 0.8393 | 3 | 0.764 | Contact Map |
| 3up1A | 2 | 0.2143 | 2.6 | 0.77 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)