| ccmD |
| ID: | 1512630596 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 69 (68) | ||
| Sequences: | 426 (272.4) | ||
| Seq/Len: | 6.265 | ||
| Nf(neff/√len): | 33.0 |
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: 6.265).
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 |
| 8_W | 12_F | 4.487 | 1.00 |
| 19_F | 23_L | 2.581 | 1.00 |
| 5_F | 35_L | 2.201 | 1.00 |
| 4_A | 52_Q | 1.705 | 1.00 |
| 37_V | 58_A | 1.599 | 1.00 |
| 45_A | 48_R | 1.579 | 0.99 |
| 5_F | 56_R | 1.532 | 0.99 |
| 4_A | 53_Q | 1.518 | 0.99 |
| 35_L | 39_S | 1.516 | 0.99 |
| 11_F | 15_G | 1.425 | 0.99 |
| 44_R | 51_A | 1.376 | 0.98 |
| 3_P | 6_A | 1.365 | 0.98 |
| 23_L | 57_E | 1.319 | 0.97 |
| 10_E | 13_A | 1.251 | 0.96 |
| 65_Q | 68_A | 1.250 | 0.96 |
| 27_M | 31_P | 1.211 | 0.95 |
| 31_P | 36_V | 1.176 | 0.94 |
| 15_G | 56_R | 1.173 | 0.94 |
| 25_V | 39_S | 1.158 | 0.93 |
| 17_Y | 25_V | 1.155 | 0.93 |
| 18_A | 32_L | 1.151 | 0.93 |
| 36_V | 40_V | 1.150 | 0.93 |
| 15_G | 23_L | 1.136 | 0.92 |
| 5_F | 39_S | 1.134 | 0.92 |
| 6_A | 10_E | 1.117 | 0.92 |
| 12_F | 19_F | 1.025 | 0.86 |
| 60_L | 63_A | 1.014 | 0.85 |
| 48_R | 58_A | 1.011 | 0.85 |
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 | |
| 4p6vB | 1 | 0.6232 | 11.6 | 0.897 | Contact Map |
| 4i5sA | 2 | 0.4783 | 9.7 | 0.901 | Contact Map |
| 5amrA | 1 | 0 | 9.1 | 0.902 | Contact Map |
| 4tllA | 2 | 0 | 8.3 | 0.904 | Contact Map |
| 4tphA | 2 | 0.6667 | 7.9 | 0.905 | Contact Map |
| 1v8kA | 1 | 0 | 7.5 | 0.906 | Contact Map |
| 4aw6A | 4 | 0.971 | 7.4 | 0.906 | Contact Map |
| 4oh3A | 2 | 0.8261 | 6.8 | 0.908 | Contact Map |
| 4pypA | 1 | 0.5942 | 5.4 | 0.912 | Contact Map |
| 5a2fA | 1 | 0 | 5.1 | 0.913 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)