| gamma_loop_align |
| ID: | 1449830601 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 46 (46) | ||
| Sequences: | 51 (25.4) | ||
| Seq/Len: | 1.109 | ||
| Nf(neff/√len): | 3.7 |
HHblits Results: (2015_06)
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: 1.109).
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 |
| 17_E | 20_L | 1.844 | 0.93 |
| 28_G | 34_R | 1.590 | 0.84 |
| 6_C | 13_V | 1.514 | 0.80 |
| 6_C | 10_G | 1.477 | 0.78 |
| 6_C | 12_C | 1.447 | 0.76 |
| 5_I | 9_N | 1.437 | 0.75 |
| 1_P | 25_T | 1.431 | 0.75 |
| 7_D | 13_V | 1.353 | 0.69 |
| 18_D | 21_F | 1.332 | 0.67 |
| 2_K | 17_E | 1.280 | 0.62 |
| 20_L | 36_M | 1.279 | 0.62 |
| 7_D | 10_G | 1.275 | 0.62 |
| 5_I | 8_I | 1.243 | 0.59 |
| 18_D | 32_V | 1.236 | 0.58 |
| 19_E | 32_V | 1.236 | 0.58 |
| 27_E | 31_T | 1.234 | 0.58 |
| 26_K | 29_K | 1.201 | 0.55 |
| 10_G | 13_V | 1.195 | 0.55 |
| 17_E | 26_K | 1.186 | 0.54 |
| 7_D | 12_C | 1.160 | 0.51 |
| 30_L | 42_P | 1.154 | 0.51 |
| 24_T | 33_E | 1.094 | 0.45 |
| 18_D | 22_R | 1.088 | 0.44 |
| 19_E | 22_R | 1.088 | 0.44 |
| 22_R | 29_K | 1.063 | 0.42 |
| 8_I | 12_C | 1.056 | 0.41 |
| 5_I | 10_G | 1.052 | 0.41 |
| 5_I | 11_K | 1.045 | 0.40 |
| 21_F | 32_V | 1.003 | 0.37 |
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 | |
| 4pmkA | 2 | 0.3478 | 5.9 | 0.863 | Contact Map |
| 4co6A | 3 | 0.9783 | 5.4 | 0.865 | Contact Map |
| 1t60C | 8 | 0.8913 | 4.8 | 0.869 | Contact Map |
| 4qxaB | 1 | 0.2391 | 3.6 | 0.876 | Contact Map |
| 1t60A | 16 | 1 | 3.2 | 0.88 | Contact Map |
| 2jnzA | 1 | 0.6304 | 3 | 0.881 | Contact Map |
| 3b8oA | 8 | 0.3478 | 2.9 | 0.882 | Contact Map |
| 3zxuB | 2 | 0 | 2.7 | 0.884 | Contact Map |
| 1bmwA | 1 | 0.7826 | 2.5 | 0.886 | Contact Map |
| 4y93A | 1 | 1 | 2.3 | 0.888 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)