| flgm |
| ID: | 1435165061 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 55 (55) | ||
| Sequences: | 940 (767.4) | ||
| Seq/Len: | 17.091 | ||
| Nf(neff/√len): | 103.5 |
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: 17.091).
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 |
| 45_D | 48_K | 3.078 | 1.00 |
| 27_S | 31_A | 3.070 | 1.00 |
| 32_A | 36_A | 2.658 | 1.00 |
| 33_I | 37_I | 2.392 | 1.00 |
| 31_A | 35_E | 2.361 | 1.00 |
| 35_E | 39_N | 2.230 | 1.00 |
| 29_K | 32_A | 2.208 | 1.00 |
| 25_F | 30_V | 1.986 | 1.00 |
| 48_K | 52_N | 1.959 | 1.00 |
| 28_A | 32_A | 1.835 | 1.00 |
| 25_F | 37_I | 1.415 | 1.00 |
| 18_E | 21_S | 1.365 | 0.99 |
| 46_P | 49_L | 1.329 | 0.99 |
| 9_S | 12_I | 1.318 | 0.99 |
| 51_D | 55_K | 1.263 | 0.99 |
| 14_E | 17_S | 1.207 | 0.98 |
| 47_E | 51_D | 1.199 | 0.98 |
| 6_S | 24_S | 1.195 | 0.98 |
| 44_V | 49_L | 1.179 | 0.98 |
| 51_D | 54_I | 1.169 | 0.97 |
| 26_D | 37_I | 1.135 | 0.97 |
| 36_A | 41_S | 1.067 | 0.95 |
| 49_L | 52_N | 1.056 | 0.95 |
| 49_L | 53_M | 1.048 | 0.94 |
| 36_A | 39_N | 1.009 | 0.93 |
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 | |
| 1rp3B | 4 | 0.9273 | 99.2 | 0.072 | Contact Map |
| 3nzzA | 2 | 0.9636 | 15.2 | 0.804 | Contact Map |
| 4iilA | 1 | 0.7091 | 13.5 | 0.809 | Contact Map |
| 4p98A | 1 | 0.8909 | 10.3 | 0.819 | Contact Map |
| 2fqxA | 1 | 0.9091 | 10.2 | 0.819 | Contact Map |
| 4pevA | 3 | 1 | 10 | 0.82 | Contact Map |
| 3h35A | 3 | 0 | 9.1 | 0.823 | Contact Map |
| 3vz6A | 1 | 0.9273 | 9 | 0.823 | Contact Map |
| 3m6cA | 1 | 0.9273 | 8.4 | 0.826 | Contact Map |
| 4v0qA | 1 | 0.8909 | 5.9 | 0.838 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)