| HELLPc |
| ID: | 1492786570 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 179 (179) | ||
| Sequences: | 525 (441.5) | ||
| Seq/Len: | 2.933 | ||
| Nf(neff/√len): | 33.0 |
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: 2.933).
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 |
| 47_A | 172_V | 2.126 | 1.00 |
| 36_K | 158_E | 2.125 | 1.00 |
| 4_A | 9_G | 2.080 | 1.00 |
| 2_E | 5_G | 2.070 | 1.00 |
| 34_G | 142_Q | 2.030 | 1.00 |
| 24_F | 172_V | 1.960 | 1.00 |
| 24_F | 168_I | 1.923 | 0.99 |
| 46_C | 85_L | 1.907 | 0.99 |
| 17_F | 55_G | 1.897 | 0.99 |
| 18_N | 22_Q | 1.892 | 0.99 |
| 55_G | 59_G | 1.863 | 0.99 |
| 103_F | 157_E | 1.727 | 0.98 |
| 51_L | 54_W | 1.718 | 0.98 |
| 50_R | 176_I | 1.701 | 0.98 |
| 43_R | 170_K | 1.613 | 0.97 |
| 34_G | 138_A | 1.608 | 0.97 |
| 3_P | 7_A | 1.564 | 0.97 |
| 55_G | 60_L | 1.550 | 0.96 |
| 50_R | 173_E | 1.519 | 0.96 |
| 82_A | 179_F | 1.519 | 0.96 |
| 100_S | 105_K | 1.518 | 0.96 |
| 25_E | 159_N | 1.507 | 0.96 |
| 44_L | 76_P | 1.481 | 0.95 |
| 54_W | 59_G | 1.475 | 0.95 |
| 93_F | 179_F | 1.472 | 0.95 |
| 5_G | 9_G | 1.450 | 0.94 |
| 8_V | 13_L | 1.386 | 0.92 |
| 102_Q | 152_K | 1.363 | 0.91 |
| 99_R | 105_K | 1.360 | 0.91 |
| 43_R | 167_D | 1.355 | 0.91 |
| 27_I | 75_S | 1.349 | 0.91 |
| 3_P | 6_L | 1.339 | 0.90 |
| 39_T | 42_L | 1.327 | 0.90 |
| 13_L | 16_L | 1.296 | 0.88 |
| 4_A | 8_V | 1.296 | 0.88 |
| 89_I | 168_I | 1.281 | 0.88 |
| 32_G | 36_K | 1.274 | 0.87 |
| 32_G | 150_K | 1.264 | 0.87 |
| 19_N | 23_C | 1.257 | 0.86 |
| 164_L | 167_D | 1.248 | 0.86 |
| 33_F | 36_K | 1.226 | 0.84 |
| 16_L | 150_K | 1.222 | 0.84 |
| 9_G | 12_A | 1.212 | 0.84 |
| 27_I | 149_E | 1.203 | 0.83 |
| 19_N | 44_L | 1.187 | 0.82 |
| 1_M | 5_G | 1.172 | 0.81 |
| 42_L | 51_L | 1.159 | 0.80 |
| 158_E | 162_G | 1.159 | 0.80 |
| 44_L | 168_I | 1.154 | 0.79 |
| 47_A | 169_T | 1.151 | 0.79 |
| 143_K | 149_E | 1.148 | 0.79 |
| 15_G | 19_N | 1.147 | 0.79 |
| 146_T | 150_K | 1.145 | 0.78 |
| 54_W | 58_L | 1.142 | 0.78 |
| 22_Q | 165_I | 1.137 | 0.78 |
| 136_K | 165_I | 1.127 | 0.77 |
| 99_R | 104_K | 1.125 | 0.77 |
| 36_K | 82_A | 1.117 | 0.76 |
| 24_F | 44_L | 1.116 | 0.76 |
| 95_I | 99_R | 1.112 | 0.76 |
| 2_E | 9_G | 1.112 | 0.76 |
| 50_R | 55_G | 1.109 | 0.75 |
| 11_L | 151_T | 1.097 | 0.74 |
| 166_E | 170_K | 1.091 | 0.74 |
| 23_C | 28_Q | 1.079 | 0.72 |
| 14_A | 146_T | 1.077 | 0.72 |
| 99_R | 160_A | 1.075 | 0.72 |
| 47_A | 52_S | 1.072 | 0.72 |
| 51_L | 55_G | 1.064 | 0.71 |
| 50_R | 57_S | 1.063 | 0.71 |
| 42_L | 53_R | 1.061 | 0.71 |
| 40_C | 79_V | 1.059 | 0.70 |
| 59_G | 175_L | 1.056 | 0.70 |
| 1_M | 6_L | 1.051 | 0.70 |
| 84_G | 145_A | 1.051 | 0.70 |
| 54_W | 60_L | 1.045 | 0.69 |
| 34_G | 145_A | 1.039 | 0.68 |
| 39_T | 88_Q | 1.033 | 0.68 |
| 174_D | 177_N | 1.032 | 0.68 |
| 151_T | 154_A | 1.026 | 0.67 |
| 27_I | 147_L | 1.022 | 0.66 |
| 82_A | 86_L | 1.020 | 0.66 |
| 34_G | 38_Q | 1.017 | 0.66 |
| 30_G | 35_S | 1.014 | 0.66 |
| 10_V | 45_D | 1.013 | 0.65 |
| 4_A | 7_A | 1.010 | 0.65 |
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 | |
| 2wvqA | 2 | 0.9274 | 100 | 0.143 | Contact Map |
| 4btfA | 1 | 0.5475 | 40.8 | 0.902 | Contact Map |
| 2msvA | 1 | 0.648 | 14.1 | 0.922 | Contact Map |
| 3he4A | 4 | 0.1676 | 10.3 | 0.926 | Contact Map |
| 3brvA | 2 | 0.1229 | 3.6 | 0.94 | Contact Map |
| 4psmA | 4 | 0.2682 | 2.9 | 0.943 | Contact Map |
| 1w3iA | 4 | 0.5419 | 2.6 | 0.945 | Contact Map |
| 1xlyA | 2 | 0.3799 | 2.5 | 0.945 | Contact Map |
| 4co6D | 3 | 0.2179 | 2.5 | 0.945 | Contact Map |
| 4pn8A | 10 | 0.1676 | 2.5 | 0.945 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)