| Jan Nowak |
| ID: | 1486483673 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (149) | ||
| Sequences: | 172 (144.6) | ||
| Seq/Len: | 1.154 | ||
| Nf(neff/√len): | 11.8 |
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: 1.154).
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 |
| 124_A | 146_A | 2.299 | 0.99 |
| 54_N | 74_G | 2.079 | 0.97 |
| 113_M | 135_V | 1.855 | 0.94 |
| 115_V | 137_V | 1.833 | 0.94 |
| 49_Q | 72_Q | 1.727 | 0.91 |
| 43_S | 65_N | 1.711 | 0.90 |
| 92_L | 115_V | 1.697 | 0.90 |
| 141_G | 144_N | 1.686 | 0.89 |
| 90_I | 113_M | 1.674 | 0.89 |
| 45_L | 58_A | 1.663 | 0.88 |
| 45_L | 137_V | 1.637 | 0.87 |
| 40_G | 43_S | 1.587 | 0.85 |
| 47_I | 70_I | 1.519 | 0.82 |
| 3_L | 9_I | 1.501 | 0.80 |
| 117_Q | 124_A | 1.476 | 0.79 |
| 92_L | 103_L | 1.447 | 0.77 |
| 60_Q | 83_Q | 1.443 | 0.77 |
| 81_V | 103_L | 1.427 | 0.76 |
| 124_A | 138_T | 1.410 | 0.74 |
| 76_G | 98_G | 1.402 | 0.74 |
| 4_L | 10_A | 1.385 | 0.72 |
| 6_V | 10_A | 1.363 | 0.71 |
| 126_V | 148_A | 1.359 | 0.70 |
| 1_M | 16_G | 1.358 | 0.70 |
| 119_G | 122_N | 1.350 | 0.70 |
| 113_M | 126_V | 1.341 | 0.69 |
| 15_S | 20_A | 1.314 | 0.67 |
| 27_G | 132_N | 1.291 | 0.65 |
| 96_G | 128_Q | 1.276 | 0.63 |
| 17_S | 20_A | 1.275 | 0.63 |
| 45_L | 68_L | 1.271 | 0.63 |
| 3_L | 10_A | 1.259 | 0.62 |
| 7_A | 18_A | 1.248 | 0.61 |
| 4_L | 13_V | 1.245 | 0.61 |
| 99_N | 122_N | 1.243 | 0.60 |
| 83_Q | 144_N | 1.239 | 0.60 |
| 127_D | 149_H | 1.232 | 0.59 |
| 122_N | 150_Q | 1.225 | 0.59 |
| 51_G | 99_N | 1.220 | 0.58 |
| 62_D | 85_S | 1.213 | 0.58 |
| 4_L | 16_G | 1.203 | 0.57 |
| 80_D | 102_T | 1.198 | 0.56 |
| 54_N | 77_N | 1.190 | 0.55 |
| 32_H | 111_S | 1.188 | 0.55 |
| 4_L | 7_A | 1.180 | 0.54 |
| 8_A | 21_G | 1.173 | 0.54 |
| 103_L | 126_V | 1.153 | 0.52 |
| 6_V | 21_G | 1.138 | 0.50 |
| 107_N | 143_G | 1.124 | 0.49 |
| 5_K | 13_V | 1.116 | 0.48 |
| 126_V | 137_V | 1.114 | 0.48 |
| 1_M | 18_A | 1.103 | 0.47 |
| 75_G | 103_L | 1.101 | 0.47 |
| 58_A | 88_S | 1.100 | 0.47 |
| 3_L | 7_A | 1.098 | 0.47 |
| 58_A | 79_A | 1.088 | 0.46 |
| 60_Q | 105_Q | 1.085 | 0.45 |
| 81_V | 92_L | 1.083 | 0.45 |
| 5_K | 9_I | 1.078 | 0.45 |
| 4_L | 9_I | 1.071 | 0.44 |
| 72_Q | 77_N | 1.060 | 0.43 |
| 130_A | 133_S | 1.056 | 0.43 |
| 79_A | 92_L | 1.056 | 0.43 |
| 43_S | 107_N | 1.055 | 0.42 |
| 7_A | 10_A | 1.054 | 0.42 |
| 2_K | 11_A | 1.048 | 0.42 |
| 40_G | 65_N | 1.041 | 0.41 |
| 117_Q | 139_Q | 1.041 | 0.41 |
| 125_A | 149_H | 1.037 | 0.41 |
| 54_N | 119_G | 1.032 | 0.40 |
| 47_I | 56_A | 1.032 | 0.40 |
| 9_I | 12_I | 1.032 | 0.40 |
| 100_S | 138_T | 1.029 | 0.40 |
| 13_V | 20_A | 1.025 | 0.40 |
| 90_I | 135_V | 1.023 | 0.39 |
| 15_S | 19_L | 1.008 | 0.38 |
| 123_G | 145_N | 1.005 | 0.38 |
| 13_V | 17_S | 1.004 | 0.38 |
| 35_G | 47_I | 1.002 | 0.38 |
| 53_G | 87_D | 1.001 | 0.37 |
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 | |
| 2vdaB | 1 | 0.1325 | 10.2 | 0.924 | Contact Map |
| 1tzsX | 1 | 0.0265 | 3.8 | 0.938 | Contact Map |
| 3zbiC | 14 | 0.1854 | 2.4 | 0.944 | Contact Map |
| 2jnaA | 2 | 0.6225 | 1.3 | 0.952 | Contact Map |
| 1m56D | 2 | 0.1391 | 1.3 | 0.953 | Contact Map |
| 1qleD | 1 | 0.1391 | 1.2 | 0.953 | Contact Map |
| 1xc0A | 1 | 0.1258 | 1 | 0.956 | Contact Map |
| 3zzhA | 4 | 0.3046 | 0.9 | 0.957 | Contact Map |
| 2esyA | 1 | 0.0662 | 0.7 | 0.96 | Contact Map |
| 2lomA | 1 | 0.2053 | 0.6 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)