| 280-335 PSI-BLAST |
| ID: | 1478539724 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 56 (55) | ||
| Sequences: | 75 (38.2) | ||
| Seq/Len: | 1.364 | ||
| Nf(neff/√len): | 5.2 |
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: 1.364).
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 |
| 5_I | 53_Y | 1.902 | 0.96 |
| 44_G | 47_T | 1.808 | 0.95 |
| 8_C | 13_I | 1.712 | 0.93 |
| 33_I | 36_K | 1.629 | 0.90 |
| 6_E | 13_I | 1.565 | 0.87 |
| 44_G | 51_Q | 1.537 | 0.86 |
| 43_H | 55_Y | 1.417 | 0.79 |
| 28_S | 33_I | 1.351 | 0.75 |
| 20_P | 25_A | 1.350 | 0.74 |
| 25_A | 51_Q | 1.314 | 0.72 |
| 41_S | 47_T | 1.286 | 0.69 |
| 43_H | 52_M | 1.271 | 0.68 |
| 13_I | 42_V | 1.260 | 0.67 |
| 45_V | 48_S | 1.259 | 0.67 |
| 43_H | 48_S | 1.254 | 0.66 |
| 35_N | 39_A | 1.249 | 0.66 |
| 40_I | 48_S | 1.228 | 0.64 |
| 33_I | 37_M | 1.188 | 0.60 |
| 34_G | 37_M | 1.158 | 0.57 |
| 31_N | 35_N | 1.154 | 0.57 |
| 31_N | 37_M | 1.120 | 0.54 |
| 15_Q | 50_G | 1.105 | 0.52 |
| 15_Q | 54_H | 1.102 | 0.52 |
| 21_V | 33_I | 1.098 | 0.51 |
| 49_G | 54_H | 1.068 | 0.48 |
| 41_S | 46_S | 1.053 | 0.47 |
| 4_F | 24_Q | 1.053 | 0.47 |
| 7_L | 11_G | 1.043 | 0.46 |
| 13_I | 52_M | 1.035 | 0.45 |
| 44_G | 48_S | 1.020 | 0.43 |
| 6_E | 43_H | 1.004 | 0.42 |
| 3_D | 22_Y | 1.001 | 0.42 |
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 | |
| 2jv3A | 1 | 0.3393 | 6.8 | 0.911 | Contact Map |
| 2j3tD | 1 | 0.3393 | 5.8 | 0.913 | Contact Map |
| 3fyrA | 3 | 0.3571 | 5 | 0.916 | Contact Map |
| 4oj5A | 3 | 0.8571 | 3.9 | 0.92 | Contact Map |
| 4g1gA | 2 | 0.8393 | 3.6 | 0.922 | Contact Map |
| 1ityA | 1 | 0.3393 | 3.4 | 0.922 | Contact Map |
| 2z84A | 1 | 0.2143 | 3.2 | 0.924 | Contact Map |
| 2yrbA | 1 | 0.8571 | 2.4 | 0.928 | Contact Map |
| 3zqjA | 6 | 0.7679 | 2.3 | 0.929 | Contact Map |
| 2fbaA | 1 | 0.8393 | 2.2 | 0.93 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)