| PrOx1 |
| ID: | 1458163206 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 78 (78) | ||
| Sequences: | 236 (147.6) | ||
| Seq/Len: | 3.026 | ||
| Nf(neff/√len): | 16.7 |
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: 3.026).
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 |
| 36_L | 40_L | 2.289 | 1.00 |
| 3_V | 18_T | 2.079 | 1.00 |
| 74_S | 77_A | 1.973 | 1.00 |
| 56_R | 73_L | 1.767 | 0.99 |
| 20_A | 41_P | 1.621 | 0.98 |
| 14_N | 76_K | 1.513 | 0.96 |
| 30_S | 37_P | 1.494 | 0.96 |
| 69_G | 72_A | 1.492 | 0.96 |
| 39_T | 42_I | 1.458 | 0.95 |
| 13_I | 56_R | 1.448 | 0.95 |
| 4_R | 14_N | 1.446 | 0.94 |
| 41_P | 49_S | 1.427 | 0.94 |
| 50_M | 76_K | 1.405 | 0.93 |
| 62_T | 65_G | 1.354 | 0.92 |
| 18_T | 58_V | 1.347 | 0.91 |
| 36_L | 49_S | 1.337 | 0.91 |
| 41_P | 44_V | 1.313 | 0.90 |
| 39_T | 75_A | 1.285 | 0.88 |
| 71_S | 76_K | 1.231 | 0.85 |
| 50_M | 74_S | 1.213 | 0.84 |
| 56_R | 67_I | 1.211 | 0.84 |
| 35_V | 69_G | 1.210 | 0.84 |
| 20_A | 23_A | 1.203 | 0.84 |
| 21_T | 68_I | 1.182 | 0.82 |
| 7_N | 53_D | 1.169 | 0.81 |
| 57_M | 71_S | 1.162 | 0.81 |
| 30_S | 34_R | 1.158 | 0.80 |
| 67_I | 70_S | 1.156 | 0.80 |
| 34_R | 43_D | 1.145 | 0.79 |
| 43_D | 47_F | 1.140 | 0.79 |
| 36_L | 44_V | 1.125 | 0.78 |
| 14_N | 34_R | 1.124 | 0.77 |
| 32_K | 47_F | 1.114 | 0.77 |
| 4_R | 65_G | 1.101 | 0.75 |
| 69_G | 74_S | 1.091 | 0.74 |
| 33_E | 65_G | 1.089 | 0.74 |
| 22_G | 35_V | 1.080 | 0.73 |
| 24_F | 56_R | 1.068 | 0.72 |
| 41_P | 51_A | 1.067 | 0.72 |
| 1_I | 6_V | 1.044 | 0.70 |
| 32_K | 76_K | 1.042 | 0.70 |
| 3_V | 44_V | 1.037 | 0.69 |
| 43_D | 68_I | 1.002 | 0.65 |
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 | |
| 3sk3A | 2 | 0.8846 | 4.2 | 0.938 | Contact Map |
| 4p61A | 2 | 0.9872 | 2.4 | 0.945 | Contact Map |
| 4g1kA | 4 | 0.7821 | 2.2 | 0.946 | Contact Map |
| 3th6A | 2 | 0.9872 | 2.2 | 0.947 | Contact Map |
| 1mo0A | 2 | 1 | 2.1 | 0.947 | Contact Map |
| 1yyaA | 2 | 0.9744 | 2 | 0.948 | Contact Map |
| 4h0pA | 2 | 0.9744 | 1.8 | 0.949 | Contact Map |
| 3gvaA | 2 | 0.4615 | 1.8 | 0.949 | Contact Map |
| 3onpA | 1 | 0.3333 | 1.5 | 0.951 | Contact Map |
| 4mfgA | 4 | 0.7564 | 1.5 | 0.951 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)