| PF08855test |
| ID: | 1495437903 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 38 (38) | ||
| Sequences: | 1495 (731.4) | ||
| Seq/Len: | 39.342 | ||
| Nf(neff/√len): | 118.6 |
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: 39.342).
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 |
| 13_L | 16_M | 2.257 | 1.00 |
| 30_L | 34_N | 1.832 | 1.00 |
| 33_E | 36_E | 1.748 | 1.00 |
| 32_T | 36_E | 1.724 | 1.00 |
| 14_K | 18_H | 1.686 | 1.00 |
| 14_K | 17_G | 1.684 | 1.00 |
| 11_W | 15_R | 1.626 | 1.00 |
| 13_L | 17_G | 1.518 | 1.00 |
| 30_L | 37_E | 1.497 | 1.00 |
| 18_H | 21_L | 1.364 | 0.99 |
| 19_Q | 22_Q | 1.347 | 0.99 |
| 8_K | 11_W | 1.315 | 0.99 |
| 16_M | 20_C | 1.263 | 0.99 |
| 32_T | 35_K | 1.190 | 0.98 |
| 17_G | 21_L | 1.164 | 0.97 |
| 5_D | 10_D | 1.128 | 0.97 |
| 29_A | 33_E | 1.103 | 0.96 |
| 31_L | 34_N | 1.086 | 0.96 |
| 4_S | 9_T | 1.079 | 0.95 |
| 17_G | 20_C | 1.079 | 0.95 |
| 15_R | 18_H | 1.057 | 0.95 |
| 12_I | 16_M | 1.041 | 0.94 |
| 10_D | 14_K | 1.038 | 0.94 |
| 9_T | 12_I | 1.023 | 0.93 |
| 25_I | 33_E | 1.020 | 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
- 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 | |
| 2dfaA | 1 | 0.7105 | 6.1 | 0.745 | Contact Map |
| 1vt0M | 12 | 0.9474 | 5.8 | 0.747 | Contact Map |
| 4mtnA | 1 | 0.7895 | 4.9 | 0.756 | Contact Map |
| 4pa0A | 2 | 0 | 4.4 | 0.76 | Contact Map |
| 2mt4A | 1 | 0.8158 | 4.1 | 0.764 | Contact Map |
| 1v6tA | 1 | 0.8947 | 4.1 | 0.764 | Contact Map |
| 2kwpA | 1 | 0.8158 | 4.1 | 0.764 | Contact Map |
| 4yknA | 1 | 0 | 4 | 0.766 | Contact Map |
| 4bfrA | 2 | 0.9737 | 4 | 0.766 | Contact Map |
| 4j4yA | 4 | 1 | 3.9 | 0.767 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)