| 1PTF_flexbb |
| ID: | 1496056269 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 489 (313.1) | ||
| Seq/Len: | 5.621 | ||
| Nf(neff/√len): | 33.6 |
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: 5.621).
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 |
| 25_S | 76_T | 2.372 | 1.00 |
| 13_A | 22_L | 2.008 | 1.00 |
| 22_L | 61_Y | 1.927 | 1.00 |
| 9_H | 50_L | 1.892 | 1.00 |
| 12_P | 16_D | 1.626 | 0.99 |
| 4_Y | 82_H | 1.587 | 0.99 |
| 5_F | 62_L | 1.505 | 0.99 |
| 6_F | 79_Q | 1.496 | 0.99 |
| 6_F | 87_A | 1.473 | 0.99 |
| 3_T | 64_L | 1.433 | 0.98 |
| 29_Y | 77_L | 1.414 | 0.98 |
| 13_A | 32_L | 1.412 | 0.98 |
| 4_Y | 74_V | 1.400 | 0.98 |
| 25_S | 51_S | 1.386 | 0.98 |
| 23_C | 87_A | 1.369 | 0.98 |
| 42_F | 48_V | 1.367 | 0.98 |
| 1_V | 64_L | 1.348 | 0.97 |
| 26_A | 77_L | 1.347 | 0.97 |
| 22_L | 81_L | 1.303 | 0.96 |
| 52_S | 77_L | 1.288 | 0.96 |
| 18_F | 35_L | 1.275 | 0.96 |
| 32_L | 86_V | 1.266 | 0.96 |
| 23_C | 29_Y | 1.212 | 0.94 |
| 60_L | 70_A | 1.177 | 0.93 |
| 37_F | 54_S | 1.175 | 0.93 |
| 69_E | 86_V | 1.168 | 0.92 |
| 50_L | 86_V | 1.164 | 0.92 |
| 1_V | 15_T | 1.154 | 0.92 |
| 4_Y | 64_L | 1.142 | 0.91 |
| 32_L | 52_S | 1.130 | 0.91 |
| 81_L | 87_A | 1.113 | 0.90 |
| 59_T | 68_D | 1.098 | 0.89 |
| 48_V | 78_I | 1.088 | 0.88 |
| 41_Y | 72_D | 1.070 | 0.87 |
| 35_L | 55_L | 1.063 | 0.87 |
| 7_K | 17_K | 1.056 | 0.86 |
| 59_T | 83_A | 1.055 | 0.86 |
| 21_L | 83_A | 1.054 | 0.86 |
| 62_L | 77_L | 1.053 | 0.86 |
| 8_I | 40_R | 1.051 | 0.86 |
| 16_D | 82_H | 1.048 | 0.86 |
| 61_Y | 78_I | 1.040 | 0.85 |
| 11_L | 18_F | 1.038 | 0.85 |
| 21_L | 43_D | 1.032 | 0.85 |
| 2_I | 62_L | 1.018 | 0.83 |
| 13_A | 23_C | 1.010 | 0.83 |
| 23_C | 55_L | 1.007 | 0.83 |
| 31_A | 78_I | 1.001 | 0.82 |
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 | |
| 1kklH | 3 | 1 | 94.6 | 0.848 | Contact Map |
| 1ka5A | 1 | 1 | 94.4 | 0.849 | Contact Map |
| 1ptfA | 1 | 1 | 94.3 | 0.85 | Contact Map |
| 3ccdA | 2 | 0.977 | 94.2 | 0.85 | Contact Map |
| 1y51A | 3 | 0.9885 | 93.8 | 0.853 | Contact Map |
| 1sphA | 2 | 0.9885 | 93.6 | 0.854 | Contact Map |
| 1pchA | 1 | 0.9885 | 93.4 | 0.855 | Contact Map |
| 3ihsA | 2 | 0.9425 | 92.8 | 0.859 | Contact Map |
| 3le1A | 2 | 0.9885 | 91.1 | 0.865 | Contact Map |
| 3wpuA | 2 | 0.7126 | 18.1 | 0.925 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)