| 8826_3 |
| ID: | 1433409549 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 62 (60) | ||
| Sequences: | 67 (38) | ||
| Seq/Len: | 1.117 | ||
| Nf(neff/√len): | 4.9 |
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: 1.117).
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 |
| 6_L | 9_E | 1.780 | 0.92 |
| 2_L | 6_L | 1.750 | 0.91 |
| 3_Q | 9_E | 1.749 | 0.91 |
| 24_K | 33_K | 1.517 | 0.81 |
| 3_Q | 6_L | 1.491 | 0.79 |
| 2_L | 9_E | 1.487 | 0.79 |
| 34_L | 37_S | 1.479 | 0.78 |
| 5_A | 8_A | 1.464 | 0.77 |
| 30_F | 50_I | 1.450 | 0.76 |
| 3_Q | 12_A | 1.447 | 0.76 |
| 12_A | 20_L | 1.420 | 0.74 |
| 25_D | 28_L | 1.402 | 0.73 |
| 42_K | 56_E | 1.373 | 0.71 |
| 22_K | 34_L | 1.357 | 0.69 |
| 43_E | 56_E | 1.240 | 0.59 |
| 3_Q | 20_L | 1.206 | 0.56 |
| 34_L | 41_N | 1.198 | 0.55 |
| 4_S | 9_E | 1.187 | 0.54 |
| 41_N | 44_L | 1.154 | 0.51 |
| 28_L | 43_E | 1.152 | 0.51 |
| 31_E | 51_L | 1.148 | 0.50 |
| 1_E | 5_A | 1.086 | 0.44 |
| 41_N | 47_E | 1.061 | 0.42 |
| 33_K | 42_K | 1.043 | 0.40 |
| 21_R | 32_S | 1.033 | 0.40 |
| 2_L | 12_A | 1.033 | 0.40 |
| 5_A | 9_E | 1.026 | 0.39 |
| 2_L | 10_I | 1.006 | 0.37 |
| 40_K | 45_L | 1.004 | 0.37 |
| 1_E | 31_E | 1.000 | 0.37 |
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 | |
| 1wt6A | 3 | 0.9677 | 93.1 | 0.701 | Contact Map |
| 4q4gX | 1 | 0 | 59.6 | 0.792 | Contact Map |
| 2dfsA | 2 | 0.9355 | 54.8 | 0.798 | Contact Map |
| 3ojaB | 1 | 0.9032 | 48.3 | 0.806 | Contact Map |
| 4cgkA | 2 | 0.8871 | 46.4 | 0.808 | Contact Map |
| 1i84S | 2 | 0 | 44.5 | 0.81 | Contact Map |
| 3q0xA | 2 | 0.9516 | 29.8 | 0.827 | Contact Map |
| 4ll8A | 1 | 0.4677 | 26.4 | 0.832 | Contact Map |
| 3hnwA | 2 | 0.9355 | 25.6 | 0.833 | Contact Map |
| 3cazA | 2 | 0.5323 | 24.6 | 0.834 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)