| 4bspA |
| ID: | 1491995294 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 88 (80) | ||
| Sequences: | 2951 (2360) | ||
| Seq/Len: | 36.888 | ||
| Nf(neff/√len): | 263.9 |
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: 36.888).
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 |
| 59_K | 62_H | 3.668 | 1.00 |
| 68_S | 71_F | 3.105 | 1.00 |
| 65_A | 74_K | 3.098 | 1.00 |
| 7_L | 16_K | 2.690 | 1.00 |
| 58_C | 66_C | 2.420 | 1.00 |
| 5_C | 8_C | 2.333 | 1.00 |
| 44_Y | 57_K | 2.271 | 1.00 |
| 64_E | 74_K | 2.044 | 1.00 |
| 63_C | 66_C | 2.007 | 1.00 |
| 14_C | 17_C | 1.904 | 1.00 |
| 10_E | 13_G | 1.903 | 1.00 |
| 72_C | 75_C | 1.897 | 1.00 |
| 47_A | 56_I | 1.849 | 1.00 |
| 42_P | 65_A | 1.845 | 1.00 |
| 64_E | 76_K | 1.776 | 1.00 |
| 5_C | 14_C | 1.750 | 1.00 |
| 63_C | 72_C | 1.743 | 1.00 |
| 6_E | 16_K | 1.726 | 1.00 |
| 59_K | 68_S | 1.668 | 1.00 |
| 21_L | 38_P | 1.655 | 1.00 |
| 18_S | 21_L | 1.637 | 1.00 |
| 62_H | 76_K | 1.551 | 1.00 |
| 24_L | 41_P | 1.493 | 1.00 |
| 4_G | 21_L | 1.434 | 1.00 |
| 58_C | 63_C | 1.354 | 0.99 |
| 6_E | 18_S | 1.311 | 0.99 |
| 22_F | 46_D | 1.305 | 0.99 |
| 45_F | 56_I | 1.301 | 0.99 |
| 7_L | 15_L | 1.274 | 0.99 |
| 65_A | 73_T | 1.195 | 0.98 |
| 76_K | 79_L | 1.162 | 0.97 |
| 82_H | 87_Y | 1.152 | 0.97 |
| 9_S | 13_G | 1.129 | 0.97 |
| 83_K | 86_C | 1.116 | 0.96 |
| 17_C | 36_C | 1.072 | 0.95 |
| 55_C | 58_C | 1.021 | 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 | |
| 4ufrB | 2 | 0 | 99.2 | 0.045 | Contact Map |
| 4c9rB | 2 | 0.9773 | 99.2 | 0.051 | Contact Map |
| 4bspA | 1 | 1 | 99.1 | 0.094 | Contact Map |
| 1igrA | 1 | 0.8068 | 98.6 | 0.257 | Contact Map |
| 1m6bA | 2 | 0.7045 | 98.5 | 0.267 | Contact Map |
| 3i2tA | 1 | 0.8295 | 98.5 | 0.268 | Contact Map |
| 2ahxA | 2 | 0.7841 | 98.4 | 0.289 | Contact Map |
| 1yy9A | 1 | 0.8068 | 98.3 | 0.321 | Contact Map |
| 1n8yC | 1 | 0.8068 | 98 | 0.359 | Contact Map |
| 2hr7A | 2 | 0.8182 | 98 | 0.359 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)