| PrOx1 |
| ID: | 1458165835 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 78 (78) | ||
| Sequences: | 402 (241.5) | ||
| Seq/Len: | 5.154 | ||
| Nf(neff/√len): | 27.3 |
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: 5.154).
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 |
| 56_R | 73_L | 2.513 | 1.00 |
| 39_T | 42_I | 2.340 | 1.00 |
| 3_V | 18_T | 2.197 | 1.00 |
| 20_A | 41_P | 1.976 | 1.00 |
| 39_T | 75_A | 1.827 | 1.00 |
| 36_L | 40_L | 1.715 | 1.00 |
| 74_S | 77_A | 1.690 | 1.00 |
| 62_T | 65_G | 1.639 | 0.99 |
| 34_R | 76_K | 1.602 | 0.99 |
| 40_L | 77_A | 1.543 | 0.99 |
| 61_N | 65_G | 1.495 | 0.99 |
| 36_L | 49_S | 1.459 | 0.98 |
| 69_G | 72_A | 1.436 | 0.98 |
| 21_T | 68_I | 1.430 | 0.98 |
| 50_M | 76_K | 1.404 | 0.98 |
| 22_G | 35_V | 1.312 | 0.96 |
| 18_T | 76_K | 1.295 | 0.96 |
| 42_I | 75_A | 1.260 | 0.95 |
| 41_P | 44_V | 1.228 | 0.94 |
| 35_V | 74_S | 1.211 | 0.93 |
| 13_I | 56_R | 1.194 | 0.92 |
| 56_R | 67_I | 1.182 | 0.92 |
| 22_G | 58_V | 1.160 | 0.91 |
| 32_K | 76_K | 1.145 | 0.90 |
| 22_G | 60_G | 1.130 | 0.89 |
| 20_A | 23_A | 1.129 | 0.89 |
| 5_T | 17_A | 1.122 | 0.89 |
| 14_N | 45_D | 1.116 | 0.89 |
| 38_H | 62_T | 1.082 | 0.86 |
| 4_R | 14_N | 1.059 | 0.85 |
| 36_L | 44_V | 1.059 | 0.85 |
| 21_T | 31_I | 1.051 | 0.84 |
| 30_S | 37_P | 1.048 | 0.84 |
| 36_L | 71_S | 1.039 | 0.83 |
| 25_N | 35_V | 1.035 | 0.83 |
| 67_I | 70_S | 1.027 | 0.82 |
| 23_A | 68_I | 1.009 | 0.81 |
| 69_G | 74_S | 1.009 | 0.81 |
| 57_M | 71_S | 1.005 | 0.80 |
| 20_A | 58_V | 1.003 | 0.80 |
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 | 2.8 | 0.942 | Contact Map |
| 3gvaA | 2 | 0.4615 | 2.8 | 0.942 | Contact Map |
| 3onpA | 1 | 0.3333 | 2 | 0.946 | Contact Map |
| 4mfgA | 4 | 0.7564 | 1.3 | 0.952 | Contact Map |
| 4h0pA | 2 | 0.9744 | 1.1 | 0.954 | Contact Map |
| 4s1pA | 1 | 0.3205 | 1.1 | 0.954 | Contact Map |
| 4g1kA | 4 | 0.8205 | 1 | 0.956 | Contact Map |
| 1e4cP | 1 | 0.4487 | 0.9 | 0.956 | Contact Map |
| 4h0oA | 2 | 0.9231 | 0.9 | 0.956 | Contact Map |
| 3ilkA | 2 | 0.3846 | 0.9 | 0.956 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)