| 1BE9_A PDZ |
| ID: | 1415847347 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 119 (100) | ||
| Sequences: | 2775 (1784.9) | ||
| Seq/Len: | 27.750 | ||
| Nf(neff/√len): | 178.5 |
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: 27.750).
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 |
| 57_L | 94_A | 4.177 | 1.00 |
| 48_G | 52_D | 2.638 | 1.00 |
| 65_S | 93_I | 2.612 | 1.00 |
| 40_I | 79_A | 2.558 | 1.00 |
| 16_R | 96_Y | 2.526 | 1.00 |
| 19_V | 91_T | 2.098 | 1.00 |
| 71_L | 79_A | 1.929 | 1.00 |
| 19_V | 89_T | 1.916 | 1.00 |
| 76_H | 80_A | 1.906 | 1.00 |
| 17_R | 93_I | 1.719 | 1.00 |
| 58_R | 96_Y | 1.650 | 1.00 |
| 34_G | 76_H | 1.628 | 1.00 |
| 33_G | 76_H | 1.580 | 1.00 |
| 26_G | 29_F | 1.515 | 1.00 |
| 32_I | 43_S | 1.508 | 1.00 |
| 42_I | 57_L | 1.473 | 1.00 |
| 26_G | 50_P | 1.408 | 1.00 |
| 71_L | 74_A | 1.383 | 0.99 |
| 74_A | 79_A | 1.381 | 0.99 |
| 65_S | 68_G | 1.341 | 0.99 |
| 62_Q | 95_Q | 1.340 | 0.99 |
| 74_A | 78_Q | 1.319 | 0.99 |
| 47_A | 52_D | 1.305 | 0.99 |
| 75_S | 78_Q | 1.301 | 0.99 |
| 39_G | 62_Q | 1.272 | 0.99 |
| 41_F | 62_Q | 1.239 | 0.98 |
| 70_D | 73_N | 1.236 | 0.98 |
| 62_Q | 97_K | 1.217 | 0.98 |
| 14_E | 98_P | 1.210 | 0.98 |
| 69_V | 82_A | 1.203 | 0.98 |
| 44_F | 59_K | 1.194 | 0.98 |
| 81_I | 85_N | 1.190 | 0.98 |
| 34_G | 40_I | 1.182 | 0.98 |
| 81_I | 84_K | 1.160 | 0.97 |
| 102_S | 107_N | 1.153 | 0.97 |
| 97_K | 100_E | 1.150 | 0.97 |
| 32_I | 76_H | 1.144 | 0.97 |
| 65_S | 70_D | 1.109 | 0.96 |
| 15_P | 64_L | 1.108 | 0.96 |
| 17_R | 91_T | 1.106 | 0.96 |
| 61_D | 96_Y | 1.093 | 0.96 |
| 40_I | 76_H | 1.084 | 0.96 |
| 29_F | 51_A | 1.077 | 0.95 |
| 100_E | 103_R | 1.062 | 0.95 |
| 71_L | 82_A | 1.053 | 0.95 |
| 66_V | 71_L | 1.042 | 0.94 |
| 30_N | 44_F | 1.034 | 0.94 |
| 45_I | 52_D | 1.024 | 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 | 0.37 | Contact Map |
| 1tp5A | 1 | 0.9664 | 99.6 | 0.383 | Contact Map |
| 1i16A | 1 | 0.9244 | 99.5 | 0.403 | Contact Map |
| 1um7A | 1 | 0.9412 | 99.5 | 0.403 | Contact Map |
| 2jikA | 2 | 0.7983 | 99.5 | 0.408 | Contact Map |
| 2enoA | 1 | 0.9328 | 99.5 | 0.408 | Contact Map |
| 2bygA | 1 | 0.7731 | 99.5 | 0.418 | Contact Map |
| 2fneA | 3 | 0.8403 | 99.5 | 0.421 | Contact Map |
| 1whaA | 1 | 0.8235 | 99.4 | 0.425 | Contact Map |
| 3b76A | 2 | 0.8151 | 99.4 | 0.426 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)