| 1BE9_A PDZ trimmed to 311-393 |
| ID: | 1416171544 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 83 (83) | ||
| Sequences: | 2319 (1487.1) | ||
| Seq/Len: | 27.940 | ||
| Nf(neff/√len): | 163.2 |
Jackhmmer Results: (2014_04_16)
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: 27.940).
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 |
| 43_L | 80_A | 3.982 | 1.00 |
| 34_G | 38_D | 2.756 | 1.00 |
| 2_R | 82_Y | 2.651 | 1.00 |
| 51_S | 79_I | 2.624 | 1.00 |
| 26_I | 65_A | 2.421 | 1.00 |
| 5_V | 77_T | 2.029 | 1.00 |
| 5_V | 75_T | 1.917 | 1.00 |
| 57_L | 65_A | 1.852 | 1.00 |
| 62_H | 66_A | 1.759 | 1.00 |
| 3_R | 79_I | 1.729 | 1.00 |
| 44_R | 82_Y | 1.653 | 1.00 |
| 20_G | 62_H | 1.548 | 1.00 |
| 18_I | 29_S | 1.511 | 1.00 |
| 57_L | 60_A | 1.449 | 1.00 |
| 33_A | 38_D | 1.423 | 1.00 |
| 19_G | 62_H | 1.398 | 0.99 |
| 28_I | 43_L | 1.395 | 0.99 |
| 56_D | 59_N | 1.348 | 0.99 |
| 67_I | 71_N | 1.307 | 0.99 |
| 51_S | 54_G | 1.305 | 0.99 |
| 60_A | 64_Q | 1.304 | 0.99 |
| 27_F | 48_Q | 1.293 | 0.99 |
| 12_G | 36_P | 1.287 | 0.99 |
| 12_G | 15_F | 1.262 | 0.99 |
| 47_D | 82_Y | 1.237 | 0.98 |
| 30_F | 45_K | 1.224 | 0.98 |
| 55_V | 68_A | 1.220 | 0.98 |
| 48_Q | 83_K | 1.216 | 0.98 |
| 61_S | 64_Q | 1.194 | 0.98 |
| 48_Q | 81_Q | 1.193 | 0.98 |
| 25_G | 48_Q | 1.179 | 0.98 |
| 1_P | 50_L | 1.162 | 0.97 |
| 3_R | 77_T | 1.157 | 0.97 |
| 51_S | 56_D | 1.119 | 0.96 |
| 60_A | 65_A | 1.117 | 0.96 |
| 67_I | 70_K | 1.104 | 0.96 |
| 15_F | 37_A | 1.100 | 0.96 |
| 20_G | 26_I | 1.031 | 0.94 |
| 57_L | 68_A | 1.029 | 0.94 |
| 26_I | 62_H | 1.023 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 2xkxA | 2 | 1 | 99.6 | 0.181 | Contact Map |
| 1z87A | 1 | 1 | 99.4 | 0.242 | Contact Map |
| 2bygA | 1 | 1 | 99.4 | 0.242 | Contact Map |
| 3gslA | 2 | 1 | 99.4 | 0.245 | Contact Map |
| 2fneA | 3 | 1 | 99.4 | 0.246 | Contact Map |
| 1i16A | 1 | 1 | 99.4 | 0.25 | Contact Map |
| 3b76A | 2 | 1 | 99.4 | 0.255 | Contact Map |
| 2jikA | 2 | 1 | 99.4 | 0.258 | Contact Map |
| 3eggC | 2 | 1 | 99.4 | 0.258 | Contact Map |
| 1um7A | 1 | 1 | 99.4 | 0.265 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)