| CSMII_2_try |
| ID: | 1475658730 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 34 (30) | ||
| Sequences: | 79 (36.3) | ||
| Seq/Len: | 2.633 | ||
| Nf(neff/√len): | 6.6 |
Jackhmmer Results: (2016_04)
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: 2.633).
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_C | 13_D | 2.522 | 1.00 |
| 11_P | 21_A | 1.817 | 0.99 |
| 12_E | 18_A | 1.636 | 0.97 |
| 6_T | 24_V | 1.620 | 0.97 |
| 16_D | 26_T | 1.406 | 0.92 |
| 11_P | 24_V | 1.345 | 0.89 |
| 4_N | 9_P | 1.224 | 0.82 |
| 22_R | 30_E | 1.222 | 0.82 |
| 5_V | 20_A | 1.199 | 0.80 |
| 16_D | 21_A | 1.178 | 0.78 |
| 23_F | 30_E | 1.157 | 0.77 |
| 12_E | 15_C | 1.152 | 0.76 |
| 8_C | 15_C | 1.146 | 0.76 |
| 10_N | 24_V | 1.119 | 0.73 |
| 12_E | 29_H | 1.090 | 0.70 |
| 3_R | 18_A | 1.076 | 0.69 |
| 7_I | 21_A | 1.062 | 0.67 |
| 2_F | 23_F | 1.017 | 0.63 |
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 | |
| 3j3ah | 1 | 0 | 5.3 | 0.865 | Contact Map |
| 3iuuA | 1 | 1 | 4.9 | 0.867 | Contact Map |
| 1qguB | 2 | 0.9706 | 4.7 | 0.868 | Contact Map |
| 3u7qB | 2 | 0.9706 | 3.5 | 0.876 | Contact Map |
| 2r7rA | 1 | 1 | 3.4 | 0.877 | Contact Map |
| 2okxA | 2 | 0.9118 | 3.1 | 0.879 | Contact Map |
| 5bpbA | 4 | 0 | 3 | 0.88 | Contact Map |
| 4emeA | 4 | 0.8824 | 2.7 | 0.882 | Contact Map |
| 4ktyA | 2 | 0.3529 | 2.7 | 0.883 | Contact Map |
| 4wziA | 2 | 0.2941 | 2.2 | 0.889 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)