| RL32 |
| ID: | 1378834714 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 57 (55) | ||
| Sequences: | 926 (535.3) | ||
| Seq/Len: | 16.836 | ||
| Nf(neff/√len): | 72.2 |
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: 16.836).
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 |
| 34_S | 44_T | 2.499 | 1.00 |
| 31_D | 34_S | 2.474 | 1.00 |
| 31_D | 44_T | 2.429 | 1.00 |
| 11_S | 15_M | 2.262 | 1.00 |
| 15_M | 18_S | 2.150 | 1.00 |
| 33_T | 48_Y | 2.147 | 1.00 |
| 34_S | 46_D | 2.116 | 1.00 |
| 28_L | 37_K | 1.903 | 1.00 |
| 31_D | 46_D | 1.876 | 1.00 |
| 12_K | 15_M | 1.828 | 1.00 |
| 30_V | 35_G | 1.811 | 1.00 |
| 39_L | 42_H | 1.770 | 1.00 |
| 10_R | 14_G | 1.765 | 1.00 |
| 8_P | 12_K | 1.720 | 1.00 |
| 24_A | 27_S | 1.701 | 1.00 |
| 3_V | 8_P | 1.637 | 1.00 |
| 30_V | 37_K | 1.564 | 1.00 |
| 43_I | 47_G | 1.294 | 0.99 |
| 29_S | 40_R | 1.232 | 0.98 |
| 4_Q | 8_P | 1.214 | 0.98 |
| 18_S | 21_A | 1.195 | 0.98 |
| 2_A | 35_G | 1.167 | 0.97 |
| 38_H | 50_R | 1.080 | 0.95 |
| 53_K | 56_A | 1.056 | 0.95 |
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 | |
| 4kix0 | 1 | 0.9825 | 99.9 | 0.043 | Contact Map |
| 2zjrZ | 1 | 0.9649 | 99.9 | 0.061 | Contact Map |
| 3v2d5 | 1 | 0.9825 | 99.9 | 0.062 | Contact Map |
| 3j3w0 | 1 | 0.9474 | 99.8 | 0.078 | Contact Map |
| 4ce45 | 1 | 0.807 | 99.6 | 0.264 | Contact Map |
| 3bbo2 | 1 | 0.8246 | 97.7 | 0.637 | Contact Map |
| 4bqqA | 2 | 0.5965 | 19.7 | 0.869 | Contact Map |
| 2apoB | 1 | 0.5614 | 18.5 | 0.871 | Contact Map |
| 1twfI | 1 | 0.5789 | 18.2 | 0.871 | Contact Map |
| 4mwaA | 8 | 0.4386 | 17.1 | 0.873 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)