| 1W4E |
| ID: | 1429471529 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 45 (42) | ||
| Sequences: | 3020 (1855.2) | ||
| Seq/Len: | 71.905 | ||
| Nf(neff/√len): | 286.3 |
HHblits Results: (2013_03)
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: 71.905).
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 |
| 20_D | 23_L | 2.648 | 1.00 |
| 12_K | 16_E | 2.546 | 1.00 |
| 35_K | 39_D | 2.281 | 1.00 |
| 9_S | 35_K | 2.246 | 1.00 |
| 23_L | 41_F | 2.142 | 1.00 |
| 13_Y | 39_D | 2.136 | 1.00 |
| 14_A | 21_I | 2.077 | 1.00 |
| 6_A | 21_I | 1.996 | 1.00 |
| 17_K | 42_L | 1.658 | 1.00 |
| 13_Y | 38_I | 1.611 | 1.00 |
| 13_Y | 17_K | 1.585 | 1.00 |
| 36_E | 40_A | 1.451 | 1.00 |
| 26_G | 33_V | 1.362 | 0.99 |
| 10_V | 35_K | 1.207 | 0.98 |
| 11_R | 15_R | 1.097 | 0.96 |
| 14_A | 33_V | 1.095 | 0.96 |
| 36_E | 39_D | 1.082 | 0.96 |
| 6_A | 11_R | 1.068 | 0.95 |
| 14_A | 19_V | 1.020 | 0.93 |
| 13_Y | 35_K | 1.008 | 0.93 |
| 26_G | 32_R | 1.008 | 0.93 |
| 17_K | 39_D | 1.005 | 0.93 |
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 | |
| 1zy8K | 5 | 0.9111 | 98.6 | -0.168 | Contact Map |
| 3dvaI | 2 | 0.9333 | 98.6 | -0.16 | Contact Map |
| 3rnmE | 2 | 0.9333 | 98.2 | -0.075 | Contact Map |
| 1w4iA | 1 | 1 | 98.2 | -0.064 | Contact Map |
| 2f60K | 1 | 1 | 98.2 | -0.06 | Contact Map |
| 2cooA | 1 | 1 | 98.2 | -0.053 | Contact Map |
| 1w85I | 2 | 0.9333 | 98.1 | -0.052 | Contact Map |
| 2eq9C | 4 | 0.8889 | 98.1 | -0.046 | Contact Map |
| 4qoyE | 2 | 0.9333 | 98.1 | -0.044 | Contact Map |
| 1balA | 1 | 1 | 98.1 | -0.031 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)