| 1ptf_-13 |
| ID: | 1502152810 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (86) | ||
| Sequences: | 426 (2.6) | ||
| Seq/Len: | 4.953 | ||
| Nf(neff/√len): | 0.3 |
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: 4.953).
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 |
| 3_A | 77_I | 6.285 | 1.00 |
| 4_N | 61_Q | 4.890 | 1.00 |
| 26_S | 58_S | 3.381 | 1.00 |
| 1_A | 70_E | 3.286 | 1.00 |
| 39_K | 51_S | 2.913 | 1.00 |
| 47_D | 58_S | 2.859 | 1.00 |
| 29_S | 67_D | 2.823 | 1.00 |
| 55_D | 58_S | 2.799 | 1.00 |
| 1_A | 31_Q | 2.381 | 1.00 |
| 19_T | 23_L | 2.329 | 1.00 |
| 26_S | 40_S | 2.276 | 1.00 |
| 26_S | 47_D | 2.098 | 1.00 |
| 26_S | 44_T | 1.939 | 1.00 |
| 74_A | 78_A | 1.896 | 1.00 |
| 40_S | 58_S | 1.868 | 1.00 |
| 3_A | 59_N | 1.763 | 1.00 |
| 1_A | 71_D | 1.689 | 0.99 |
| 58_S | 61_Q | 1.611 | 0.99 |
| 31_Q | 61_Q | 1.592 | 0.99 |
| 40_S | 47_D | 1.537 | 0.99 |
| 36_Y | 58_S | 1.535 | 0.99 |
| 31_Q | 40_S | 1.521 | 0.99 |
| 4_N | 31_Q | 1.476 | 0.98 |
| 26_S | 31_Q | 1.454 | 0.98 |
| 33_E | 44_T | 1.288 | 0.95 |
| 3_A | 67_D | 1.245 | 0.94 |
| 27_S | 40_S | 1.240 | 0.94 |
| 4_N | 40_S | 1.233 | 0.93 |
| 1_A | 4_N | 1.231 | 0.93 |
| 1_A | 33_E | 1.209 | 0.92 |
| 26_S | 33_E | 1.190 | 0.92 |
| 31_Q | 58_S | 1.181 | 0.91 |
| 55_D | 78_A | 1.179 | 0.91 |
| 26_S | 61_Q | 1.126 | 0.88 |
| 44_T | 58_S | 1.105 | 0.87 |
| 39_K | 82_E | 1.086 | 0.86 |
| 58_S | 67_D | 1.053 | 0.83 |
| 33_E | 58_S | 1.031 | 0.82 |
| 58_S | 78_A | 1.027 | 0.81 |
| 35_L | 77_I | 1.005 | 0.79 |
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 | |
| 1kklH | 3 | 1 | 99.3 | 0.692 | Contact Map |
| 1ptfA | 1 | 1 | 99.2 | 0.694 | Contact Map |
| 1ka5A | 1 | 1 | 99.2 | 0.696 | Contact Map |
| 1pchA | 1 | 1 | 99.2 | 0.697 | Contact Map |
| 1y51A | 3 | 1 | 99.2 | 0.7 | Contact Map |
| 1sphA | 2 | 1 | 99.2 | 0.7 | Contact Map |
| 3ihsA | 2 | 0.9419 | 99.2 | 0.7 | Contact Map |
| 3ccdA | 2 | 0.9767 | 99.2 | 0.7 | Contact Map |
| 3le1A | 2 | 0.9884 | 99.1 | 0.71 | Contact Map |
| 1yx5B | 1 | 0.7558 | 34.5 | 0.924 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)