| student |
| ID: | 1504548454 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 71 (68) | ||
| Sequences: | 607 (529.6) | ||
| Seq/Len: | 8.926 | ||
| Nf(neff/√len): | 64.2 |
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: 8.926).
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 |
| 17_S | 49_S | 4.267 | 1.00 |
| 21_V | 53_G | 3.282 | 1.00 |
| 23_L | 55_L | 3.112 | 1.00 |
| 24_K | 56_K | 2.433 | 1.00 |
| 25_R | 57_R | 2.419 | 1.00 |
| 28_L | 60_L | 2.216 | 1.00 |
| 18_T | 50_T | 1.955 | 1.00 |
| 10_N | 16_N | 1.891 | 1.00 |
| 4_K | 38_N | 1.805 | 1.00 |
| 29_R | 61_K | 1.789 | 1.00 |
| 39_A | 47_V | 1.752 | 1.00 |
| 20_A | 59_I | 1.484 | 1.00 |
| 11_D | 35_N | 1.454 | 1.00 |
| 56_K | 60_L | 1.351 | 0.99 |
| 22_A | 54_I | 1.327 | 0.99 |
| 43_E | 66_L | 1.225 | 0.98 |
| 40_D | 44_D | 1.194 | 0.97 |
| 63_I | 66_L | 1.187 | 0.97 |
| 15_V | 58_Y | 1.179 | 0.97 |
| 52_L | 56_K | 1.167 | 0.97 |
| 26_Y | 36_T | 1.165 | 0.97 |
| 15_V | 55_L | 1.162 | 0.97 |
| 9_V | 23_L | 1.147 | 0.96 |
| 27_V | 59_I | 1.140 | 0.96 |
| 57_R | 62_E | 1.122 | 0.96 |
| 66_L | 69_K | 1.122 | 0.96 |
| 20_A | 24_K | 1.117 | 0.96 |
| 20_A | 52_L | 1.105 | 0.95 |
| 34_I | 38_N | 1.105 | 0.95 |
| 14_K | 46_R | 1.101 | 0.95 |
| 27_V | 52_L | 1.087 | 0.95 |
| 16_N | 48_N | 1.059 | 0.94 |
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 | |
| 1daqA | 1 | 1 | 99.7 | -0.002 | Contact Map |
| 2yikA | 1 | 0 | 99.6 | 0.031 | Contact Map |
| 4cj0A | 1 | 0 | 99.6 | 0.065 | Contact Map |
| 4fl4A | 4 | 0.9014 | 99.5 | 0.098 | Contact Map |
| 4uypB | 2 | 0.9718 | 99.5 | 0.104 | Contact Map |
| 2y3nB | 2 | 0.8451 | 99.5 | 0.107 | Contact Map |
| 4dh2B | 2 | 0.9577 | 99.5 | 0.11 | Contact Map |
| 2vn6B | 1 | 0.9014 | 99.5 | 0.13 | Contact Map |
| 3kcpA | 1 | 0.9296 | 99.3 | 0.203 | Contact Map |
| 2cclB | 2 | 0.8451 | 99.3 | 0.214 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)