| OMPR_ECOLI |
| ID: | 1430407950 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 76 (76) | ||
| Sequences: | 15894 (10998.9) | ||
| Seq/Len: | 209.132 | ||
| Nf(neff/√len): | 1261.7 |
HHblits Results: (2013_03)
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: 209.132).
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 |
| 27_R | 47_D | 3.497 | 1.00 |
| 15_K | 19_S | 3.057 | 1.00 |
| 16_A | 33_L | 3.052 | 1.00 |
| 70_V | 76_V | 2.415 | 1.00 |
| 44_R | 47_D | 2.401 | 1.00 |
| 10_E | 56_M | 2.171 | 1.00 |
| 9_G | 12_A | 2.042 | 1.00 |
| 29_K | 33_L | 1.960 | 1.00 |
| 20_H | 23_E | 1.957 | 1.00 |
| 48_V | 51_S | 1.938 | 1.00 |
| 68_Q | 76_V | 1.851 | 1.00 |
| 16_A | 30_L | 1.831 | 1.00 |
| 26_S | 29_K | 1.748 | 1.00 |
| 8_S | 12_A | 1.747 | 1.00 |
| 16_A | 25_L | 1.730 | 1.00 |
| 21_P | 25_L | 1.642 | 1.00 |
| 9_G | 35_R | 1.603 | 1.00 |
| 24_P | 73_L | 1.599 | 1.00 |
| 16_A | 20_H | 1.515 | 1.00 |
| 49_Q | 52_R | 1.486 | 1.00 |
| 27_R | 43_E | 1.482 | 1.00 |
| 9_G | 49_Q | 1.425 | 1.00 |
| 24_P | 70_V | 1.419 | 1.00 |
| 51_S | 55_R | 1.399 | 0.99 |
| 13_V | 49_Q | 1.394 | 0.99 |
| 45_S | 49_Q | 1.327 | 0.99 |
| 12_A | 15_K | 1.230 | 0.98 |
| 23_E | 29_K | 1.203 | 0.98 |
| 48_V | 52_R | 1.173 | 0.98 |
| 25_L | 29_K | 1.142 | 0.97 |
| 8_S | 73_L | 1.142 | 0.97 |
| 6_L | 53_L | 1.140 | 0.97 |
| 47_D | 71_W | 1.106 | 0.96 |
| 20_H | 25_L | 1.105 | 0.96 |
| 50_I | 75_Y | 1.088 | 0.96 |
| 16_A | 29_K | 1.081 | 0.95 |
| 7_T | 56_M | 1.032 | 0.94 |
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 | |
| 2zxjA | 2 | 1 | 99.8 | -0.077 | Contact Map |
| 4nhjA | 2 | 1 | 99.8 | -0.062 | Contact Map |
| 3q9vA | 2 | 0.9868 | 99.7 | 0.016 | Contact Map |
| 4ixaA | 2 | 1 | 99.7 | 0.018 | Contact Map |
| 2k4jA | 1 | 1 | 99.7 | 0.021 | Contact Map |
| 2hwvA | 1 | 1 | 99.7 | 0.021 | Contact Map |
| 1opcA | 1 | 1 | 99.7 | 0.024 | Contact Map |
| 3zq7A | 1 | 1 | 99.7 | 0.028 | Contact Map |
| 2pmuA | 6 | 0.9737 | 99.7 | 0.039 | Contact Map |
| 2jzyA | 1 | 0.9868 | 99.7 | 0.042 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)