| FKRP_251_318 -force run |
| ID: | 1483300993 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 68 (68) | ||
| Sequences: | 63 (45) | ||
| Seq/Len: | 0.926 | ||
| Nf(neff/√len): | 5.5 |
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: 0.926).
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 |
| 26_L | 34_L | 2.072 | 0.96 |
| 4_R | 50_V | 1.557 | 0.78 |
| 18_L | 41_K | 1.483 | 0.73 |
| 14_R | 37_F | 1.472 | 0.73 |
| 8_E | 20_R | 1.457 | 0.72 |
| 58_L | 63_W | 1.443 | 0.71 |
| 54_T | 63_W | 1.439 | 0.70 |
| 42_E | 59_Y | 1.372 | 0.65 |
| 20_R | 37_F | 1.365 | 0.64 |
| 4_R | 8_E | 1.352 | 0.63 |
| 22_L | 52_G | 1.342 | 0.62 |
| 42_E | 62_R | 1.307 | 0.59 |
| 36_W | 39_C | 1.258 | 0.55 |
| 36_W | 47_F | 1.249 | 0.54 |
| 19_L | 25_R | 1.218 | 0.51 |
| 4_R | 52_G | 1.217 | 0.51 |
| 1_A | 7_A | 1.206 | 0.50 |
| 5_W | 58_L | 1.184 | 0.48 |
| 29_W | 41_K | 1.176 | 0.48 |
| 49_T | 53_D | 1.175 | 0.47 |
| 22_L | 31_G | 1.171 | 0.47 |
| 55_P | 64_T | 1.133 | 0.44 |
| 55_P | 65_P | 1.133 | 0.44 |
| 55_P | 66_P | 1.133 | 0.44 |
| 57_Y | 64_T | 1.133 | 0.44 |
| 57_Y | 65_P | 1.133 | 0.44 |
| 57_Y | 66_P | 1.133 | 0.44 |
| 2_H | 49_T | 1.120 | 0.43 |
| 28_S | 43_T | 1.118 | 0.42 |
| 2_H | 48_G | 1.113 | 0.42 |
| 20_R | 54_T | 1.109 | 0.42 |
| 49_T | 63_W | 1.101 | 0.41 |
| 28_S | 37_F | 1.095 | 0.40 |
| 6_K | 18_L | 1.086 | 0.40 |
| 2_H | 63_W | 1.076 | 0.39 |
| 25_R | 31_G | 1.076 | 0.39 |
| 47_F | 58_L | 1.061 | 0.37 |
| 26_L | 51_V | 1.049 | 0.36 |
| 2_H | 5_W | 1.044 | 0.36 |
| 41_K | 63_W | 1.042 | 0.36 |
| 9_R | 41_K | 1.018 | 0.34 |
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 | |
| 1wqbA | 1 | 0.2794 | 10.5 | 0.922 | Contact Map |
| 5aj3U | 1 | 0 | 6.5 | 0.929 | Contact Map |
| 3cg7A | 2 | 0.9412 | 6.4 | 0.929 | Contact Map |
| 2wr1A | 3 | 0.9118 | 4.9 | 0.933 | Contact Map |
| 2gfqA | 3 | 0.4412 | 4.7 | 0.934 | Contact Map |
| 4g38A | 1 | 0.5441 | 4.4 | 0.935 | Contact Map |
| 1mkeA | 1 | 0.7353 | 3.7 | 0.937 | Contact Map |
| 4dk2A | 1 | 0.4559 | 3.7 | 0.937 | Contact Map |
| 3t7vA | 1 | 0.5294 | 3.2 | 0.939 | Contact Map |
| 3bzcA | 1 | 0.8382 | 3.1 | 0.939 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)