| 1PTF_fixbb |
| ID: | 1496056308 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 338 (17) | ||
| Seq/Len: | 3.885 | ||
| Nf(neff/√len): | 1.8 |
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: 3.885).
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 |
| 49_A | 78_I | 2.939 | 1.00 |
| 59_A | 83_L | 2.553 | 1.00 |
| 57_Q | 77_I | 2.251 | 1.00 |
| 11_E | 57_Q | 2.065 | 1.00 |
| 20_A | 24_K | 1.920 | 1.00 |
| 27_S | 31_S | 1.840 | 1.00 |
| 17_E | 34_V | 1.666 | 0.99 |
| 49_A | 83_L | 1.643 | 0.99 |
| 34_V | 40_R | 1.609 | 0.99 |
| 10_A | 68_P | 1.498 | 0.97 |
| 56_V | 59_A | 1.479 | 0.97 |
| 18_A | 31_S | 1.440 | 0.96 |
| 18_A | 66_Y | 1.416 | 0.96 |
| 8_V | 40_R | 1.362 | 0.95 |
| 34_V | 71_T | 1.345 | 0.94 |
| 78_I | 83_L | 1.339 | 0.94 |
| 41_Q | 83_L | 1.337 | 0.94 |
| 16_G | 34_V | 1.320 | 0.94 |
| 4_C | 71_T | 1.308 | 0.93 |
| 17_E | 51_A | 1.306 | 0.93 |
| 59_A | 71_T | 1.287 | 0.92 |
| 4_C | 7_L | 1.270 | 0.92 |
| 62_N | 77_I | 1.252 | 0.91 |
| 47_V | 64_E | 1.242 | 0.90 |
| 20_A | 48_D | 1.236 | 0.90 |
| 20_A | 47_V | 1.212 | 0.89 |
| 72_E | 77_I | 1.209 | 0.89 |
| 4_C | 84_N | 1.203 | 0.89 |
| 12_K | 60_I | 1.203 | 0.89 |
| 59_A | 78_I | 1.202 | 0.88 |
| 18_A | 27_S | 1.186 | 0.88 |
| 16_G | 85_N | 1.186 | 0.88 |
| 64_E | 72_E | 1.175 | 0.87 |
| 31_S | 66_Y | 1.170 | 0.87 |
| 15_T | 57_Q | 1.144 | 0.85 |
| 5_Q | 48_D | 1.136 | 0.84 |
| 8_V | 57_Q | 1.131 | 0.84 |
| 3_S | 72_E | 1.127 | 0.84 |
| 30_S | 40_R | 1.104 | 0.82 |
| 41_Q | 49_A | 1.103 | 0.82 |
| 12_K | 36_E | 1.097 | 0.81 |
| 27_S | 51_A | 1.097 | 0.81 |
| 3_S | 84_N | 1.073 | 0.79 |
| 51_A | 72_E | 1.040 | 0.76 |
| 8_V | 20_A | 1.037 | 0.76 |
| 64_E | 77_I | 1.024 | 0.75 |
| 79_N | 84_N | 1.023 | 0.75 |
| 28_K | 36_E | 1.015 | 0.74 |
| 12_K | 51_A | 1.011 | 0.73 |
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 | 98.9 | 0.741 | Contact Map |
| 1pchA | 1 | 0.9885 | 98.9 | 0.747 | Contact Map |
| 1ka5A | 1 | 1 | 98.9 | 0.747 | Contact Map |
| 3ihsA | 2 | 0.9425 | 98.8 | 0.751 | Contact Map |
| 1sphA | 2 | 0.9885 | 98.8 | 0.751 | Contact Map |
| 1ptfA | 1 | 1 | 98.8 | 0.752 | Contact Map |
| 1y51A | 3 | 0.9885 | 98.8 | 0.753 | Contact Map |
| 3ccdA | 2 | 0.977 | 98.8 | 0.754 | Contact Map |
| 3le1A | 2 | 0.9885 | 98.7 | 0.762 | Contact Map |
| 4ryaA | 1 | 0.3448 | 12.7 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)