| Chris Graham PrOx proper |
| ID: | 1458524750 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 43 (43) | ||
| Sequences: | 1179 (457.8) | ||
| Seq/Len: | 27.419 | ||
| Nf(neff/√len): | 69.8 |
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: 27.419).
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 |
| 24_T | 27_I | 3.499 | 1.00 |
| 7_L | 20_D | 2.426 | 1.00 |
| 5_A | 26_A | 1.993 | 1.00 |
| 21_P | 25_E | 1.981 | 1.00 |
| 26_A | 36_I | 1.905 | 1.00 |
| 14_A | 32_F | 1.685 | 1.00 |
| 5_A | 24_T | 1.461 | 1.00 |
| 15_L | 18_A | 1.373 | 0.99 |
| 21_P | 34_S | 1.327 | 0.99 |
| 25_E | 29_E | 1.304 | 0.99 |
| 7_L | 41_L | 1.246 | 0.98 |
| 25_E | 38_E | 1.211 | 0.98 |
| 22_P | 38_E | 1.193 | 0.98 |
| 20_D | 35_N | 1.172 | 0.98 |
| 3_T | 43_A | 1.118 | 0.96 |
| 26_A | 34_S | 1.102 | 0.96 |
| 36_I | 39_T | 1.091 | 0.96 |
| 33_D | 38_E | 1.077 | 0.95 |
| 1_I | 24_T | 1.070 | 0.95 |
| 16_N | 37_S | 1.053 | 0.95 |
| 30_E | 33_D | 1.041 | 0.94 |
| 11_G | 22_P | 1.000 | 0.92 |
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 | |
| 2pigA | 2 | 0.6512 | 3 | 0.89 | Contact Map |
| 3floB | 4 | 0.1395 | 2.2 | 0.898 | Contact Map |
| 4hicA | 2 | 0 | 1.8 | 0.902 | Contact Map |
| 4rgkA | 1 | 0.5116 | 1.8 | 0.903 | Contact Map |
| 4x8eA | 2 | 0.9535 | 1.6 | 0.904 | Contact Map |
| 1y4jA | 2 | 0.9535 | 1.5 | 0.907 | Contact Map |
| 4exwA | 5 | 0.1163 | 1.4 | 0.909 | Contact Map |
| 1z70X | 1 | 0.9535 | 1.3 | 0.909 | Contact Map |
| 3kioA | 1 | 0.3953 | 1.3 | 0.911 | Contact Map |
| 4l6yA | 2 | 0 | 1.2 | 0.912 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)