| 1PTF_flex_2x_bl |
| ID: | 1497960066 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 87 (87) | ||
| Sequences: | 515 (435.6) | ||
| Seq/Len: | 5.920 | ||
| Nf(neff/√len): | 46.7 |
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: 5.920).
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 |
| 4_C | 78_I | 2.143 | 1.00 |
| 32_E | 50_L | 1.850 | 1.00 |
| 25_T | 76_V | 1.775 | 1.00 |
| 56_S | 63_I | 1.668 | 1.00 |
| 35_L | 55_P | 1.362 | 0.98 |
| 5_M | 40_F | 1.350 | 0.98 |
| 15_S | 76_V | 1.348 | 0.98 |
| 49_V | 53_S | 1.285 | 0.96 |
| 37_L | 44_M | 1.283 | 0.96 |
| 34_M | 60_I | 1.268 | 0.96 |
| 14_V | 47_T | 1.230 | 0.95 |
| 16_A | 31_V | 1.217 | 0.95 |
| 21_K | 73_A | 1.205 | 0.94 |
| 11_A | 33_I | 1.203 | 0.94 |
| 12_E | 35_L | 1.195 | 0.94 |
| 25_T | 32_E | 1.186 | 0.94 |
| 41_Y | 54_N | 1.176 | 0.93 |
| 8_V | 73_A | 1.151 | 0.92 |
| 43_D | 53_S | 1.149 | 0.92 |
| 68_P | 71_T | 1.147 | 0.92 |
| 6_F | 42_F | 1.144 | 0.92 |
| 10_V | 18_Y | 1.139 | 0.92 |
| 29_K | 83_T | 1.132 | 0.92 |
| 6_F | 66_Y | 1.132 | 0.92 |
| 1_Y | 32_E | 1.120 | 0.91 |
| 24_E | 76_V | 1.101 | 0.90 |
| 36_L | 57_L | 1.074 | 0.88 |
| 5_M | 42_F | 1.073 | 0.88 |
| 66_Y | 71_T | 1.071 | 0.88 |
| 21_K | 84_L | 1.066 | 0.88 |
| 22_V | 81_L | 1.061 | 0.88 |
| 17_E | 21_K | 1.059 | 0.88 |
| 37_L | 55_P | 1.056 | 0.87 |
| 28_T | 85_N | 1.047 | 0.87 |
| 19_A | 30_E | 1.043 | 0.86 |
| 46_D | 72_E | 1.041 | 0.86 |
| 20_Y | 25_T | 1.040 | 0.86 |
| 4_C | 34_M | 1.039 | 0.86 |
| 8_V | 19_A | 1.037 | 0.86 |
| 63_I | 73_A | 1.035 | 0.86 |
| 18_Y | 47_T | 1.035 | 0.86 |
| 23_S | 49_V | 1.029 | 0.85 |
| 13_G | 30_E | 1.029 | 0.85 |
| 17_E | 63_I | 1.026 | 0.85 |
| 1_Y | 53_S | 1.021 | 0.85 |
| 22_V | 31_V | 1.018 | 0.85 |
| 3_A | 47_T | 1.016 | 0.84 |
| 16_A | 29_K | 1.015 | 0.84 |
| 71_T | 85_N | 1.014 | 0.84 |
| 9_K | 48_S | 1.009 | 0.84 |
| 1_Y | 6_F | 1.006 | 0.84 |
| 6_F | 35_L | 1.005 | 0.84 |
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 | |
| 3ccdA | 2 | 0.977 | 94.7 | 0.823 | Contact Map |
| 1kklH | 3 | 1 | 93.3 | 0.833 | Contact Map |
| 3ihsA | 2 | 0.9425 | 92.4 | 0.838 | Contact Map |
| 1ka5A | 1 | 1 | 92.3 | 0.839 | Contact Map |
| 1ptfA | 1 | 1 | 91.8 | 0.841 | Contact Map |
| 1pchA | 1 | 0.9885 | 91 | 0.844 | Contact Map |
| 1y51A | 3 | 0.9885 | 90.7 | 0.845 | Contact Map |
| 1sphA | 2 | 0.9885 | 90.6 | 0.845 | Contact Map |
| 3le1A | 2 | 0.9885 | 89.2 | 0.85 | Contact Map |
| 4umaA | 4 | 0.8851 | 5.6 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)