| hfq PA14 |
| ID: | 1435000452 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 82 (73) | ||
| Sequences: | 353 (160.3) | ||
| Seq/Len: | 4.836 | ||
| Nf(neff/√len): | 18.8 |
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: 4.836).
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 |
| 44_I | 59_I | 3.556 | 1.00 |
| 13_N | 39_F | 2.804 | 1.00 |
| 13_N | 16_R | 1.935 | 1.00 |
| 28_N | 61_T | 1.838 | 1.00 |
| 43_V | 53_M | 1.748 | 1.00 |
| 31_K | 50_V | 1.683 | 0.99 |
| 13_N | 17_K | 1.668 | 0.99 |
| 7_L | 62_V | 1.608 | 0.99 |
| 18_E | 66_R | 1.519 | 0.99 |
| 32_L | 52_Q | 1.434 | 0.98 |
| 32_L | 46_L | 1.416 | 0.97 |
| 24_I | 69_R | 1.401 | 0.97 |
| 28_N | 43_V | 1.319 | 0.96 |
| 37_E | 47_K | 1.273 | 0.94 |
| 21_P | 66_R | 1.272 | 0.94 |
| 7_L | 64_P | 1.220 | 0.93 |
| 45_L | 52_Q | 1.210 | 0.92 |
| 36_I | 46_L | 1.205 | 0.92 |
| 27_V | 60_S | 1.178 | 0.91 |
| 28_N | 60_S | 1.171 | 0.90 |
| 14_T | 18_E | 1.158 | 0.90 |
| 15_L | 22_V | 1.154 | 0.90 |
| 41_Q | 63_V | 1.142 | 0.89 |
| 25_Y | 44_I | 1.141 | 0.89 |
| 7_L | 24_I | 1.130 | 0.88 |
| 31_K | 43_V | 1.130 | 0.88 |
| 19_R | 35_Q | 1.127 | 0.88 |
| 30_I | 49_T | 1.089 | 0.86 |
| 6_S | 41_Q | 1.082 | 0.85 |
| 1_M | 70_L | 1.080 | 0.85 |
| 33_Q | 50_V | 1.080 | 0.85 |
| 44_I | 63_V | 1.078 | 0.85 |
| 1_M | 15_L | 1.076 | 0.85 |
| 55_Y | 63_V | 1.073 | 0.84 |
| 36_I | 48_N | 1.054 | 0.83 |
| 5_H | 24_I | 1.054 | 0.83 |
| 18_E | 39_F | 1.037 | 0.82 |
| 31_K | 51_S | 1.030 | 0.81 |
| 14_T | 69_R | 1.025 | 0.81 |
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 | |
| 2y90A | 1 | 0.7805 | 100 | 0.149 | Contact Map |
| 1u1sA | 6 | 0.8293 | 100 | 0.168 | Contact Map |
| 3sb2A | 6 | 0.8415 | 100 | 0.202 | Contact Map |
| 3ahuA | 3 | 0.7927 | 100 | 0.216 | Contact Map |
| 1kq1A | 12 | 0.7927 | 100 | 0.218 | Contact Map |
| 4pnoA | 1 | 0.7805 | 100 | 0.231 | Contact Map |
| 4nl2D | 6 | 0.8902 | 100 | 0.232 | Contact Map |
| 3hfoA | 3 | 0.7561 | 99.9 | 0.39 | Contact Map |
| 4x9cA | 6 | 0.7195 | 99.9 | 0.398 | Contact Map |
| 3hfnA | 2 | 0.7195 | 99.9 | 0.399 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)