| CDI |
| ID: | 1450196053 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 33 (33) | ||
| Sequences: | 334 (227.9) | ||
| Seq/Len: | 10.121 | ||
| Nf(neff/√len): | 39.7 |
HHblits Results: (2015_06)
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: 10.121).
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 |
| 11_T | 16_A | 2.001 | 1.00 |
| 12_K | 22_F | 1.684 | 1.00 |
| 8_T | 14_A | 1.677 | 1.00 |
| 8_T | 11_T | 1.648 | 1.00 |
| 4_P | 7_P | 1.603 | 1.00 |
| 6_S | 19_L | 1.406 | 0.99 |
| 29_E | 32_E | 1.403 | 0.99 |
| 13_A | 25_P | 1.340 | 0.99 |
| 19_L | 23_N | 1.290 | 0.99 |
| 15_L | 26_L | 1.243 | 0.98 |
| 10_H | 15_L | 1.181 | 0.98 |
| 27_R | 31_L | 1.176 | 0.98 |
| 16_A | 19_L | 1.143 | 0.97 |
| 29_E | 33_K | 1.134 | 0.97 |
| 3_K | 20_D | 1.121 | 0.97 |
| 30_S | 33_K | 1.081 | 0.95 |
| 14_A | 22_F | 1.064 | 0.95 |
| 17_D | 23_N | 1.010 | 0.93 |
| 17_D | 28_S | 1.006 | 0.93 |
| 1_A | 21_I | 1.005 | 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 | |
| 4gmoA | 1 | 1 | 2.9 | 0.765 | Contact Map |
| 4l9pB | 1 | 0.6061 | 2.5 | 0.771 | Contact Map |
| 4yfkD | 2 | 0.3636 | 2.5 | 0.772 | Contact Map |
| 4ce4F | 1 | 0.6667 | 1.8 | 0.788 | Contact Map |
| 1puoA | 2 | 1 | 1.8 | 0.788 | Contact Map |
| 3bboG | 1 | 0.7273 | 1.8 | 0.789 | Contact Map |
| 3m1iB | 1 | 0 | 1.5 | 0.797 | Contact Map |
| 3zdlB | 1 | 0.5152 | 1.5 | 0.797 | Contact Map |
| 4tp9E | 1 | 0.697 | 1.5 | 0.8 | Contact Map |
| 4ndjA | 1 | 0.7879 | 1.4 | 0.8 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)