| CDI_x |
| ID: | 1452538867 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 32 (25) | ||
| Sequences: | 96 (42.2) | ||
| Seq/Len: | 3.840 | ||
| Nf(neff/√len): | 8.4 |
Jackhmmer Results: (2015_08)
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: 3.840).
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 |
| 10_H | 17_F | 2.130 | 1.00 |
| 5_P | 19_M | 2.082 | 1.00 |
| 23_Q | 26_T | 1.611 | 0.99 |
| 11_T | 16_G | 1.563 | 0.98 |
| 20_N | 23_Q | 1.515 | 0.98 |
| 9_V | 13_E | 1.383 | 0.95 |
| 21_M | 24_A | 1.379 | 0.95 |
| 12_K | 28_P | 1.364 | 0.95 |
| 9_V | 15_L | 1.338 | 0.94 |
| 10_H | 14_A | 1.329 | 0.94 |
| 11_T | 17_F | 1.310 | 0.93 |
| 22_F | 25_P | 1.289 | 0.92 |
| 25_P | 29_D | 1.260 | 0.91 |
| 20_N | 24_A | 1.219 | 0.89 |
| 11_T | 26_T | 1.169 | 0.86 |
| 5_P | 25_P | 1.150 | 0.85 |
| 17_F | 23_Q | 1.143 | 0.85 |
| 12_K | 16_G | 1.014 | 0.73 |
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 | |
| 3tutA | 1 | 1 | 8.2 | 0.84 | Contact Map |
| 3j32A | 2 | 1 | 7.2 | 0.845 | Contact Map |
| 4o89A | 2 | 1 | 5.5 | 0.852 | Contact Map |
| 1vw3D | 1 | 0.7812 | 5.5 | 0.853 | Contact Map |
| 4clqA | 1 | 1 | 5.3 | 0.854 | Contact Map |
| 3j21D | 1 | 0.7188 | 4.7 | 0.857 | Contact Map |
| 1lnlA | 3 | 0.4375 | 4.7 | 0.857 | Contact Map |
| 3zdlB | 1 | 0.5 | 3.9 | 0.863 | Contact Map |
| 4wzzA | 1 | 0.6875 | 3.8 | 0.864 | Contact Map |
| 3p24A | 4 | 1 | 3.6 | 0.865 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)