| sandwich |
| ID: | 1473155194 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 50 (48) | ||
| Sequences: | 576 (413.7) | ||
| Seq/Len: | 12.000 | ||
| Nf(neff/√len): | 59.7 |
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: 12.000).
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 |
| 18_P | 21_K | 2.399 | 1.00 |
| 19_S | 24_V | 2.044 | 1.00 |
| 13_K | 21_K | 1.703 | 1.00 |
| 23_S | 26_I | 1.661 | 1.00 |
| 1_G | 4_P | 1.654 | 1.00 |
| 6_P | 10_A | 1.639 | 1.00 |
| 2_D | 5_P | 1.456 | 1.00 |
| 1_G | 5_P | 1.431 | 1.00 |
| 43_P | 46_D | 1.405 | 0.99 |
| 19_S | 41_F | 1.327 | 0.99 |
| 30_G | 33_Q | 1.293 | 0.99 |
| 8_V | 16_S | 1.215 | 0.98 |
| 6_P | 9_P | 1.203 | 0.98 |
| 41_F | 44_F | 1.201 | 0.98 |
| 8_V | 15_K | 1.171 | 0.98 |
| 12_K | 44_F | 1.153 | 0.97 |
| 13_K | 46_D | 1.151 | 0.97 |
| 2_D | 41_F | 1.135 | 0.97 |
| 13_K | 26_I | 1.127 | 0.97 |
| 12_K | 21_K | 1.083 | 0.96 |
| 19_S | 39_P | 1.049 | 0.94 |
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 | |
| 4bl0B | 2 | 0 | 5.5 | 0.76 | Contact Map |
| 3nttA | 1 | 0.92 | 2 | 0.808 | Contact Map |
| 2lsnA | 1 | 0.34 | 2 | 0.81 | Contact Map |
| 3ng9A | 10 | 0.92 | 1.9 | 0.81 | Contact Map |
| 1z14A | 1 | 1 | 1.9 | 0.811 | Contact Map |
| 1okiA | 2 | 0.32 | 1.9 | 0.811 | Contact Map |
| 2g8gA | 1 | 0.92 | 1.8 | 0.812 | Contact Map |
| 4iovA | 1 | 0.92 | 1.8 | 0.812 | Contact Map |
| 1s58A | 1 | 0.92 | 1.5 | 0.823 | Contact Map |
| 2yseA | 1 | 0.46 | 1.3 | 0.827 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)