| fliacwgrem |
| ID: | 1430149511 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 34 (34) | ||
| Sequences: | 3890 (3174.6) | ||
| Seq/Len: | 114.412 | ||
| Nf(neff/√len): | 544.4 |
HHblits Results: (2013_03)
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: 114.412).
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 |
| 20_T | 25_V | 3.355 | 1.00 |
| 5_N | 33_V | 3.048 | 1.00 |
| 1_Q | 6_K | 2.947 | 1.00 |
| 19_I | 28_F | 2.615 | 1.00 |
| 18_F | 25_V | 2.497 | 1.00 |
| 2_I | 9_F | 2.347 | 1.00 |
| 8_Y | 19_I | 1.972 | 1.00 |
| 29_N | 33_V | 1.801 | 1.00 |
| 8_Y | 21_I | 1.791 | 1.00 |
| 10_D | 14_I | 1.496 | 1.00 |
| 20_T | 23_D | 1.470 | 1.00 |
| 20_T | 24_K | 1.408 | 1.00 |
| 21_I | 28_F | 1.379 | 0.99 |
| 1_Q | 4_D | 1.151 | 0.97 |
| 2_I | 5_N | 1.067 | 0.95 |
| 1_Q | 5_N | 1.031 | 0.94 |
| 7_Y | 33_V | 1.023 | 0.93 |
| 9_F | 15_M | 1.001 | 0.92 |
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 | |
| 3klkA | 1 | 1 | 98.7 | 0.099 | Contact Map |
| 2bibA | 1 | 1 | 98.6 | 0.114 | Contact Map |
| 3hiaA | 3 | 1 | 98.6 | 0.116 | Contact Map |
| 4nc2A | 1 | 1 | 98.6 | 0.125 | Contact Map |
| 4nbxA | 1 | 1 | 98.6 | 0.127 | Contact Map |
| 2j8gA | 1 | 1 | 98.5 | 0.146 | Contact Map |
| 3ttqA | 1 | 1 | 98.5 | 0.147 | Contact Map |
| 1h8gA | 2 | 1 | 98.5 | 0.159 | Contact Map |
| 4iwtA | 2 | 1 | 98.4 | 0.161 | Contact Map |
| 4np4A | 1 | 1 | 98.4 | 0.166 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)