| pengfei tian |
| ID: | 1471301151 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 35 (35) | ||
| Sequences: | 40 (35.3) | ||
| Seq/Len: | 1.143 | ||
| Nf(neff/√len): | 6.0 |
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: 1.143).
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_Y | 31_K | 2.271 | 0.99 |
| 19_Y | 33_E | 2.106 | 0.98 |
| 21_D | 29_W | 1.713 | 0.90 |
| 16_Y | 29_W | 1.639 | 0.87 |
| 20_Y | 27_S | 1.596 | 0.85 |
| 9_E | 30_E | 1.372 | 0.71 |
| 3_S | 6_R | 1.342 | 0.69 |
| 8_V | 22_L | 1.330 | 0.68 |
| 13_S | 29_W | 1.245 | 0.60 |
| 5_G | 16_Y | 1.238 | 0.60 |
| 18_Y | 26_A | 1.228 | 0.59 |
| 17_H | 35_F | 1.194 | 0.55 |
| 24_S | 29_W | 1.173 | 0.53 |
| 11_I | 29_W | 1.147 | 0.51 |
| 14_E | 21_D | 1.128 | 0.49 |
| 25_G | 35_F | 1.096 | 0.46 |
| 5_G | 28_Q | 1.094 | 0.46 |
| 24_S | 30_E | 1.050 | 0.42 |
| 12_T | 15_G | 1.048 | 0.41 |
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 | |
| 1eg3A | 1 | 1 | 99.2 | 0.094 | Contact Map |
| 3l4hA | 1 | 1 | 99.1 | 0.124 | Contact Map |
| 3olmA | 1 | 1 | 99.1 | 0.15 | Contact Map |
| 2jmfA | 1 | 1 | 99.1 | 0.153 | Contact Map |
| 2yseA | 1 | 1 | 99 | 0.156 | Contact Map |
| 1wmvA | 1 | 1 | 99 | 0.159 | Contact Map |
| 2ysdA | 1 | 1 | 99 | 0.16 | Contact Map |
| 2ysbA | 1 | 1 | 99 | 0.163 | Contact Map |
| 1i5hW | 1 | 1 | 99 | 0.17 | Contact Map |
| 1jmqA | 1 | 1 | 99 | 0.174 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)