| spind 1-70 |
| ID: | 1447772111 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 70 (64) | ||
| Sequences: | 366 (193.1) | ||
| Seq/Len: | 5.719 | ||
| Nf(neff/√len): | 24.1 |
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: 5.719).
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 |
| 47_E | 57_Q | 1.848 | 1.00 |
| 22_K | 26_Y | 1.837 | 1.00 |
| 19_E | 26_Y | 1.713 | 1.00 |
| 53_E | 60_Y | 1.518 | 0.99 |
| 16_A | 22_K | 1.464 | 0.99 |
| 47_E | 56_E | 1.414 | 0.98 |
| 25_Q | 63_Q | 1.411 | 0.98 |
| 4_D | 7_T | 1.386 | 0.98 |
| 60_Y | 65_E | 1.349 | 0.97 |
| 18_E | 28_L | 1.321 | 0.97 |
| 17_E | 30_L | 1.309 | 0.97 |
| 57_Q | 60_Y | 1.305 | 0.97 |
| 22_K | 28_L | 1.275 | 0.96 |
| 45_R | 58_E | 1.274 | 0.96 |
| 16_A | 33_S | 1.232 | 0.95 |
| 57_Q | 61_T | 1.220 | 0.94 |
| 53_E | 57_Q | 1.203 | 0.94 |
| 16_A | 19_E | 1.178 | 0.93 |
| 8_N | 12_R | 1.145 | 0.92 |
| 11_C | 14_K | 1.138 | 0.91 |
| 19_E | 28_L | 1.138 | 0.91 |
| 8_N | 16_A | 1.134 | 0.91 |
| 26_Y | 29_Q | 1.124 | 0.91 |
| 23_A | 59_K | 1.105 | 0.90 |
| 9_L | 33_S | 1.100 | 0.89 |
| 6_I | 11_C | 1.097 | 0.89 |
| 23_A | 41_L | 1.089 | 0.89 |
| 19_E | 38_Q | 1.075 | 0.88 |
| 61_T | 65_E | 1.069 | 0.88 |
| 50_T | 58_E | 1.043 | 0.86 |
| 56_E | 66_V | 1.039 | 0.85 |
| 20_R | 32_E | 1.021 | 0.84 |
| 5_I | 8_N | 1.012 | 0.83 |
| 36_E | 42_D | 1.007 | 0.83 |
| 16_A | 28_L | 1.003 | 0.83 |
| 19_E | 22_K | 1.002 | 0.83 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2bnxA | 2 | 0.2143 | 37.3 | 0.816 | Contact Map |
| 4psmA | 4 | 0.8571 | 15.6 | 0.847 | Contact Map |
| 2dfsA | 2 | 1 | 12.3 | 0.854 | Contact Map |
| 3hnwA | 2 | 0.7286 | 8.5 | 0.864 | Contact Map |
| 4xa4A | 2 | 0 | 8.2 | 0.865 | Contact Map |
| 4ll8A | 1 | 0.0143 | 8 | 0.865 | Contact Map |
| 1i84S | 2 | 0 | 7.4 | 0.867 | Contact Map |
| 1nyhA | 1 | 0.8714 | 6.8 | 0.87 | Contact Map |
| 2j5uA | 2 | 0.5429 | 6.3 | 0.872 | Contact Map |
| 3o0zA | 4 | 1 | 6.3 | 0.872 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)