| CcmD-01 |
| ID: | 1517604753 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 69 (63) | ||
| Sequences: | 724 (510.9) | ||
| Seq/Len: | 11.492 | ||
| Nf(neff/√len): | 64.4 |
Jackhmmer Results: (2016_04)
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: 11.492).
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 | 4.410 | 1.00 |
| 19_F | 23_L | 2.980 | 1.00 |
| 35_L | 39_S | 2.083 | 1.00 |
| 5_F | 35_L | 2.020 | 1.00 |
| 14_M | 22_W | 1.702 | 1.00 |
| 43_H | 47_L | 1.646 | 1.00 |
| 4_A | 53_Q | 1.641 | 1.00 |
| 3_P | 6_A | 1.585 | 1.00 |
| 30_I | 34_V | 1.580 | 1.00 |
| 26_V | 30_I | 1.455 | 1.00 |
| 6_A | 10_E | 1.448 | 1.00 |
| 17_Y | 23_L | 1.304 | 0.99 |
| 5_F | 39_S | 1.266 | 0.99 |
| 60_L | 63_A | 1.263 | 0.99 |
| 5_F | 56_R | 1.260 | 0.99 |
| 17_Y | 24_A | 1.254 | 0.99 |
| 14_M | 21_V | 1.242 | 0.98 |
| 37_V | 58_A | 1.210 | 0.98 |
| 27_M | 64_Q | 1.166 | 0.97 |
| 23_L | 35_L | 1.158 | 0.97 |
| 61_R | 64_Q | 1.150 | 0.97 |
| 52_Q | 61_R | 1.127 | 0.97 |
| 10_E | 13_A | 1.109 | 0.96 |
| 31_P | 39_S | 1.045 | 0.94 |
| 14_M | 20_F | 1.038 | 0.94 |
| 40_V | 62_A | 1.021 | 0.93 |
| 46_I | 50_V | 1.011 | 0.93 |
| 10_E | 42_Q | 1.004 | 0.93 |
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 | |
| 4tllA | 2 | 0.0145 | 22.8 | 0.878 | Contact Map |
| 4aw6A | 4 | 0.971 | 17.6 | 0.884 | Contact Map |
| 2kncB | 1 | 0.8406 | 11.9 | 0.893 | Contact Map |
| 4i5sA | 2 | 0.4783 | 10.2 | 0.896 | Contact Map |
| 5amrA | 1 | 0 | 9 | 0.898 | Contact Map |
| 4tphA | 2 | 0.6667 | 6.6 | 0.905 | Contact Map |
| 4p6vB | 1 | 0.6232 | 6.6 | 0.905 | Contact Map |
| 4tllB | 2 | 0.0435 | 6.5 | 0.905 | Contact Map |
| 3sksA | 1 | 0.7536 | 5.7 | 0.907 | Contact Map |
| 4u2pA | 4 | 0.5507 | 5.7 | 0.907 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)