| 197 |
| ID: | 1485535898 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 52 (52) | ||
| Sequences: | 417 (334.5) | ||
| Seq/Len: | 8.019 | ||
| Nf(neff/√len): | 46.4 |
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: 8.019).
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 |
| 41_L | 49_W | 2.222 | 1.00 |
| 15_G | 18_T | 2.126 | 1.00 |
| 44_N | 48_H | 1.935 | 1.00 |
| 39_G | 51_Y | 1.791 | 1.00 |
| 8_D | 22_A | 1.667 | 1.00 |
| 36_G | 51_Y | 1.665 | 1.00 |
| 6_G | 23_D | 1.600 | 1.00 |
| 12_V | 20_T | 1.485 | 0.99 |
| 8_D | 12_V | 1.425 | 0.99 |
| 8_D | 11_A | 1.383 | 0.99 |
| 3_T | 43_I | 1.347 | 0.99 |
| 6_G | 9_D | 1.339 | 0.99 |
| 11_A | 29_F | 1.327 | 0.99 |
| 39_G | 47_G | 1.288 | 0.98 |
| 11_A | 27_N | 1.265 | 0.98 |
| 24_N | 27_N | 1.252 | 0.98 |
| 34_L | 37_Q | 1.242 | 0.98 |
| 4_I | 9_D | 1.220 | 0.97 |
| 1_T | 14_S | 1.202 | 0.97 |
| 15_G | 33_S | 1.167 | 0.96 |
| 17_S | 37_Q | 1.163 | 0.96 |
| 34_L | 44_N | 1.153 | 0.96 |
| 38_F | 51_Y | 1.149 | 0.96 |
| 47_G | 51_Y | 1.140 | 0.95 |
| 3_T | 9_D | 1.070 | 0.93 |
| 20_T | 33_S | 1.066 | 0.93 |
| 9_D | 23_D | 1.047 | 0.92 |
| 43_I | 47_G | 1.045 | 0.92 |
| 42_S | 52_T | 1.040 | 0.91 |
| 25_G | 28_Q | 1.015 | 0.90 |
| 11_A | 26_Q | 1.006 | 0.89 |
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 | |
| 1l3wA | 1 | 0.9808 | 58.8 | 0.668 | Contact Map |
| 3q2vA | 2 | 1 | 56.1 | 0.674 | Contact Map |
| 3q2wA | 1 | 1 | 48.5 | 0.688 | Contact Map |
| 1q55A | 4 | 0.9808 | 45.2 | 0.694 | Contact Map |
| 4p99A | 4 | 0.9615 | 34.3 | 0.714 | Contact Map |
| 4lm8A | 1 | 0.9615 | 29.4 | 0.724 | Contact Map |
| 2yn5A | 2 | 0.8846 | 28.4 | 0.726 | Contact Map |
| 3ubhA | 1 | 1 | 27.6 | 0.727 | Contact Map |
| 3mvsA | 1 | 1 | 21.5 | 0.742 | Contact Map |
| 3ubfA | 1 | 1 | 14.3 | 0.762 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)