| wieslaw2 |
| ID: | 1427834008 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 45 (45) | ||
| Sequences: | 123 (103.7) | ||
| Seq/Len: | 2.733 | ||
| Nf(neff/√len): | 15.5 |
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: 2.733).
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 |
| 8_I | 32_V | 2.894 | 1.00 |
| 5_A | 29_V | 2.664 | 1.00 |
| 18_L | 42_I | 2.586 | 1.00 |
| 13_R | 37_E | 2.541 | 1.00 |
| 3_N | 27_N | 2.208 | 1.00 |
| 10_T | 34_G | 2.111 | 1.00 |
| 16_V | 40_V | 1.508 | 0.95 |
| 17_Q | 41_L | 1.489 | 0.95 |
| 14_A | 38_S | 1.424 | 0.93 |
| 6_K | 30_E | 1.371 | 0.91 |
| 4_S | 7_D | 1.331 | 0.89 |
| 14_A | 40_V | 1.261 | 0.85 |
| 6_K | 35_K | 1.146 | 0.77 |
| 6_K | 32_V | 1.088 | 0.71 |
| 3_N | 20_N | 1.051 | 0.67 |
| 9_R | 33_V | 1.048 | 0.67 |
| 32_V | 38_S | 1.046 | 0.67 |
| 21_V | 45_E | 1.040 | 0.66 |
| 20_N | 44_N | 1.039 | 0.66 |
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 | |
| 2kj3A | 3 | 1 | 96.3 | 0.419 | Contact Map |
| 1us2A | 1 | 0.8222 | 3.7 | 0.817 | Contact Map |
| 2cpiA | 1 | 0.5111 | 2.1 | 0.839 | Contact Map |
| 1peqA | 1 | 1 | 1.8 | 0.845 | Contact Map |
| 3k8tA | 1 | 1 | 1.6 | 0.848 | Contact Map |
| 3hncA | 2 | 1 | 1.5 | 0.852 | Contact Map |
| 2dh8A | 1 | 0.5333 | 1.3 | 0.857 | Contact Map |
| 2e5hA | 1 | 0.5333 | 1.3 | 0.859 | Contact Map |
| 3o0qA | 2 | 1 | 1.2 | 0.859 | Contact Map |
| 1x4dA | 1 | 0.5111 | 1.2 | 0.86 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)