| PHF10-PHD |
| ID: | 1488489972 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 100 (100) | ||
| Sequences: | 894 (565.4) | ||
| Seq/Len: | 8.940 | ||
| Nf(neff/√len): | 56.5 |
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: 8.940).
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 |
| 2_C | 5_C | 3.093 | 1.00 |
| 25_Q | 51_Q | 2.630 | 1.00 |
| 58_C | 61_C | 2.603 | 1.00 |
| 52_C | 55_C | 2.444 | 1.00 |
| 87_L | 91_P | 2.285 | 1.00 |
| 81_H | 84_C | 2.070 | 1.00 |
| 97_C | 100_C | 2.048 | 1.00 |
| 73_C | 76_C | 1.997 | 1.00 |
| 23_C | 26_C | 1.948 | 1.00 |
| 70_M | 79_G | 1.826 | 1.00 |
| 22_H | 29_S | 1.669 | 1.00 |
| 74_D | 91_P | 1.667 | 1.00 |
| 31_H | 34_C | 1.664 | 1.00 |
| 50_W | 55_C | 1.637 | 1.00 |
| 75_M | 96_I | 1.599 | 1.00 |
| 34_C | 52_C | 1.522 | 1.00 |
| 69_E | 83_F | 1.509 | 1.00 |
| 73_C | 84_C | 1.425 | 0.99 |
| 31_H | 55_C | 1.396 | 0.99 |
| 73_C | 81_H | 1.383 | 0.99 |
| 76_C | 84_C | 1.363 | 0.99 |
| 95_W | 100_C | 1.352 | 0.99 |
| 22_H | 27_E | 1.345 | 0.99 |
| 34_C | 55_C | 1.343 | 0.99 |
| 76_C | 81_H | 1.255 | 0.98 |
| 26_C | 34_C | 1.249 | 0.98 |
| 61_C | 97_C | 1.208 | 0.98 |
| 76_C | 97_C | 1.194 | 0.97 |
| 26_C | 52_C | 1.180 | 0.97 |
| 7_K | 12_N | 1.171 | 0.97 |
| 61_C | 76_C | 1.168 | 0.97 |
| 44_M | 47_T | 1.158 | 0.97 |
| 48_Y | 78_R | 1.148 | 0.96 |
| 31_H | 52_C | 1.115 | 0.96 |
| 84_C | 97_C | 1.114 | 0.95 |
| 71_M | 74_D | 1.102 | 0.95 |
| 61_C | 84_C | 1.090 | 0.95 |
| 26_C | 55_C | 1.069 | 0.94 |
| 3_G | 6_L | 1.046 | 0.93 |
| 81_H | 97_C | 1.042 | 0.93 |
| 4_I | 7_K | 1.034 | 0.93 |
| 80_Y | 98_D | 1.028 | 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 | |
| 2kwjA | 1 | 1 | 99.9 | 0.169 | Contact Map |
| 3v43A | 1 | 1 | 99.9 | 0.196 | Contact Map |
| 4lk9A | 1 | 1 | 99.9 | 0.202 | Contact Map |
| 2ysmA | 1 | 0.91 | 99.8 | 0.272 | Contact Map |
| 2lbmA | 1 | 0.88 | 99.6 | 0.378 | Contact Map |
| 4gneA | 1 | 0.81 | 99.6 | 0.404 | Contact Map |
| 3ql9A | 1 | 0.78 | 99.6 | 0.406 | Contact Map |
| 4tvrA | 1 | 0 | 99.4 | 0.461 | Contact Map |
| 3shbA | 1 | 0.63 | 99.2 | 0.519 | Contact Map |
| 3aslA | 1 | 0.62 | 99.1 | 0.54 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)