| cut filtered growth hormone manual |
| ID: | 1465212855 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (56) | ||
| Sequences: | 311 (208.9) | ||
| Seq/Len: | 5.554 | ||
| Nf(neff/√len): | 27.9 |
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: 5.554).
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 | 2.043 | 1.00 |
| 3_L | 50_L | 1.789 | 1.00 |
| 1_V | 50_L | 1.780 | 1.00 |
| 52_P | 55_V | 1.624 | 0.99 |
| 1_V | 4_P | 1.526 | 0.99 |
| 37_F | 44_R | 1.511 | 0.99 |
| 1_V | 27_I | 1.508 | 0.99 |
| 30_L | 39_F | 1.435 | 0.98 |
| 22_I | 29_G | 1.331 | 0.97 |
| 36_V | 55_V | 1.315 | 0.97 |
| 3_L | 41_K | 1.262 | 0.95 |
| 45_I | 53_V | 1.260 | 0.95 |
| 45_I | 51_P | 1.201 | 0.94 |
| 34_L | 53_V | 1.191 | 0.93 |
| 17_F | 28_F | 1.188 | 0.93 |
| 15_F | 34_L | 1.188 | 0.93 |
| 7_S | 49_I | 1.145 | 0.91 |
| 19_W | 37_F | 1.141 | 0.91 |
| 13_E | 17_F | 1.130 | 0.91 |
| 47_M | 50_L | 1.118 | 0.90 |
| 29_G | 40_S | 1.115 | 0.90 |
| 41_K | 47_M | 1.108 | 0.89 |
| 34_L | 39_F | 1.088 | 0.88 |
| 2_T | 7_S | 1.068 | 0.87 |
| 1_V | 55_V | 1.068 | 0.87 |
| 33_M | 36_V | 1.064 | 0.87 |
| 1_V | 43_Q | 1.053 | 0.86 |
| 14_D | 22_I | 1.051 | 0.86 |
| 16_Y | 30_L | 1.046 | 0.85 |
| 27_I | 32_V | 1.036 | 0.85 |
| 47_M | 56_P | 1.036 | 0.85 |
| 28_F | 35_F | 1.024 | 0.84 |
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 | 27 | 0.689 | Contact Map |
| 3lb6C | 1 | 0 | 21 | 0.705 | Contact Map |
| 1q55A | 4 | 0.1964 | 14 | 0.728 | Contact Map |
| 2k9yA | 2 | 0.7143 | 6.5 | 0.765 | Contact Map |
| 4ev6A | 5 | 0.7321 | 5.4 | 0.774 | Contact Map |
| 4i0uA | 10 | 0.6964 | 5.2 | 0.775 | Contact Map |
| 3j8f7 | 1 | 0.0893 | 4.8 | 0.78 | Contact Map |
| 3ayfA | 1 | 0.9821 | 3.4 | 0.795 | Contact Map |
| 2mk9A | 2 | 0.6071 | 2.8 | 0.803 | Contact Map |
| 2jwaA | 2 | 0.75 | 2.5 | 0.808 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)