| sigma |
| ID: | 1489757710 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 40 (40) | ||
| Sequences: | 52 (48) | ||
| Seq/Len: | 1.300 | ||
| Nf(neff/√len): | 7.6 |
HHblits Results: (2016_02)
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: 1.300).
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 |
| 19_Q | 27_Q | 2.312 | 0.99 |
| 5_N | 28_V | 1.764 | 0.93 |
| 12_F | 19_Q | 1.603 | 0.88 |
| 4_N | 38_Q | 1.600 | 0.88 |
| 30_G | 35_G | 1.573 | 0.87 |
| 26_N | 40_G | 1.527 | 0.85 |
| 10_N | 23_Q | 1.510 | 0.84 |
| 26_N | 30_G | 1.485 | 0.82 |
| 2_S | 5_N | 1.436 | 0.79 |
| 17_G | 25_G | 1.413 | 0.78 |
| 15_T | 29_S | 1.283 | 0.68 |
| 32_N | 35_G | 1.280 | 0.67 |
| 18_T | 31_G | 1.247 | 0.64 |
| 21_I | 27_Q | 1.240 | 0.64 |
| 6_L | 15_T | 1.210 | 0.61 |
| 8_S | 38_Q | 1.189 | 0.59 |
| 24_G | 33_F | 1.171 | 0.57 |
| 18_T | 34_N | 1.166 | 0.57 |
| 10_N | 22_N | 1.104 | 0.51 |
| 14_A | 40_G | 1.074 | 0.48 |
| 9_G | 12_F | 1.068 | 0.47 |
| 8_S | 23_Q | 1.067 | 0.47 |
| 25_G | 28_V | 1.027 | 0.43 |
| 33_F | 39_F | 1.011 | 0.41 |
| 30_G | 33_F | 1.002 | 0.40 |
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 | |
| 3rlfF | 1 | 1 | 1.4 | 0.856 | Contact Map |
| 3t41A | 2 | 1 | 1.1 | 0.867 | Contact Map |
| 2b6nA | 1 | 1 | 0.8 | 0.876 | Contact Map |
| 4tr2A | 2 | 1 | 0.8 | 0.881 | Contact Map |
| 2wq4A | 3 | 0.125 | 0.7 | 0.881 | Contact Map |
| 3i26A | 4 | 0.675 | 0.7 | 0.883 | Contact Map |
| 4c7lA | 2 | 0.675 | 0.7 | 0.884 | Contact Map |
| 3i1kA | 3 | 0.675 | 0.7 | 0.884 | Contact Map |
| 1flcA | 3 | 0.675 | 0.7 | 0.884 | Contact Map |
| 1to2E | 1 | 1 | 0.7 | 0.884 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)