| DVL1_PDZ |
| ID: | 1402405941 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 73 (72) | ||
| Sequences: | 5505 (3365.5) | ||
| Seq/Len: | 76.458 | ||
| Nf(neff/√len): | 396.6 |
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: 76.458).
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 |
| 36_G | 40_A | 3.126 | 1.00 |
| 28_I | 67_A | 2.770 | 1.00 |
| 59_F | 67_A | 2.634 | 1.00 |
| 59_F | 62_M | 2.399 | 1.00 |
| 64_N | 68_V | 2.381 | 1.00 |
| 18_G | 64_N | 2.299 | 1.00 |
| 63_S | 66_D | 2.166 | 1.00 |
| 62_M | 66_D | 2.096 | 1.00 |
| 35_K | 40_A | 2.041 | 1.00 |
| 29_Y | 50_M | 1.974 | 1.00 |
| 57_V | 70_V | 1.919 | 1.00 |
| 17_V | 31_G | 1.903 | 1.00 |
| 16_I | 68_V | 1.713 | 1.00 |
| 69_R | 73_E | 1.599 | 1.00 |
| 66_D | 69_R | 1.461 | 1.00 |
| 53_Q | 56_D | 1.443 | 1.00 |
| 58_N | 61_N | 1.426 | 1.00 |
| 62_M | 70_V | 1.419 | 1.00 |
| 30_I | 45_I | 1.381 | 0.99 |
| 27_G | 50_M | 1.360 | 0.99 |
| 62_M | 67_A | 1.302 | 0.99 |
| 28_I | 64_N | 1.265 | 0.99 |
| 32_S | 47_P | 1.224 | 0.98 |
| 11_F | 38_A | 1.216 | 0.98 |
| 33_I | 47_P | 1.186 | 0.98 |
| 15_S | 32_S | 1.183 | 0.98 |
| 10_H | 41_A | 1.166 | 0.97 |
| 15_S | 34_M | 1.136 | 0.97 |
| 54_V | 59_F | 1.114 | 0.96 |
| 19_Q | 28_I | 1.111 | 0.96 |
| 17_V | 34_M | 1.092 | 0.96 |
| 4_L | 39_V | 1.089 | 0.96 |
| 53_Q | 58_N | 1.070 | 0.95 |
| 69_R | 72_R | 1.068 | 0.95 |
| 16_I | 19_Q | 1.054 | 0.95 |
| 59_F | 70_V | 1.014 | 0.93 |
| 33_I | 40_A | 1.004 | 0.93 |
| 39_V | 45_I | 1.002 | 0.92 |
| 65_D | 69_R | 1.001 | 0.92 |
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 | |
| 2xkxA | 2 | 0.9863 | 99.3 | 0.214 | Contact Map |
| 3suzA | 1 | 0.9589 | 99.3 | 0.246 | Contact Map |
| 1z87A | 1 | 0.9726 | 99.2 | 0.248 | Contact Map |
| 3k1rA | 1 | 0.9589 | 99.2 | 0.262 | Contact Map |
| 1wfgA | 1 | 1 | 99.2 | 0.275 | Contact Map |
| 3b76A | 2 | 1 | 99.2 | 0.276 | Contact Map |
| 2bygA | 1 | 0.9863 | 99.2 | 0.279 | Contact Map |
| 1wg6A | 1 | 1 | 99.2 | 0.279 | Contact Map |
| 2lobA | 1 | 0.9726 | 99.1 | 0.285 | Contact Map |
| 3cbzA | 1 | 1 | 99.1 | 0.285 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)