| PfCSP_324_412 |
| ID: | 1493598549 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 88 (79) | ||
| Sequences: | 147 (105.2) | ||
| Seq/Len: | 1.861 | ||
| Nf(neff/√len): | 11.8 |
Jackhmmer Results: (2016_04)
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: 1.861).
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 |
| 19_S | 38_K | 3.138 | 1.00 |
| 34_Q | 58_K | 3.019 | 1.00 |
| 17_S | 38_K | 2.235 | 1.00 |
| 38_K | 54_D | 1.789 | 0.97 |
| 29_C | 32_G | 1.527 | 0.91 |
| 17_S | 54_D | 1.498 | 0.90 |
| 17_S | 40_G | 1.456 | 0.88 |
| 6_H | 9_Q | 1.450 | 0.88 |
| 19_S | 54_D | 1.425 | 0.87 |
| 29_C | 65_C | 1.388 | 0.85 |
| 31_N | 61_K | 1.350 | 0.82 |
| 18_L | 23_S | 1.347 | 0.82 |
| 9_Q | 13_T | 1.342 | 0.82 |
| 16_N | 40_G | 1.304 | 0.79 |
| 78_L | 81_V | 1.293 | 0.78 |
| 27_V | 62_M | 1.285 | 0.78 |
| 60_C | 65_C | 1.284 | 0.78 |
| 6_H | 12_K | 1.270 | 0.77 |
| 70_N | 75_S | 1.258 | 0.76 |
| 6_H | 10_Y | 1.233 | 0.74 |
| 22_W | 36_R | 1.233 | 0.74 |
| 21_E | 58_K | 1.157 | 0.67 |
| 38_K | 71_V | 1.150 | 0.66 |
| 77_G | 81_V | 1.110 | 0.62 |
| 8_E | 15_K | 1.099 | 0.61 |
| 74_S | 80_M | 1.085 | 0.59 |
| 72_V | 75_S | 1.081 | 0.59 |
| 75_S | 78_L | 1.078 | 0.59 |
| 10_Y | 14_I | 1.067 | 0.57 |
| 32_G | 65_C | 1.067 | 0.57 |
| 72_V | 77_G | 1.061 | 0.57 |
| 4_D | 8_E | 1.061 | 0.57 |
| 11_L | 14_I | 1.056 | 0.56 |
| 22_W | 76_I | 1.053 | 0.56 |
| 78_L | 82_L | 1.047 | 0.55 |
| 20_T | 79_I | 1.034 | 0.54 |
| 8_E | 13_T | 1.025 | 0.53 |
| 75_S | 82_L | 1.022 | 0.53 |
| 30_G | 58_K | 1.016 | 0.52 |
| 26_S | 70_N | 1.011 | 0.51 |
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 | |
| 3vdjA | 1 | 0.7614 | 99.5 | 0.446 | Contact Map |
| 1vexA | 1 | 0.6364 | 99.1 | 0.536 | Contact Map |
| 3t5oA | 1 | 0.875 | 99.1 | 0.537 | Contact Map |
| 1lslA | 1 | 0.7386 | 99 | 0.548 | Contact Map |
| 3ghmA | 1 | 0.9886 | 99 | 0.551 | Contact Map |
| 1szlA | 1 | 0.6818 | 99 | 0.553 | Contact Map |
| 2rjqA | 1 | 0.0114 | 99 | 0.563 | Contact Map |
| 3r6bA | 1 | 0.75 | 98.8 | 0.584 | Contact Map |
| 1w0rA | 2 | 1 | 98.6 | 0.614 | Contact Map |
| 4okuA | 2 | 0.7614 | 98.5 | 0.63 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)