| 1fvg |
| ID: | 1492603391 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 199 (185) | ||
| Sequences: | 4136 (2399.2) | ||
| Seq/Len: | 22.357 | ||
| Nf(neff/√len): | 176.4 |
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: 22.357).
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 |
| 46_A | 108_F | 3.916 | 1.00 |
| 147_V | 151_L | 3.840 | 1.00 |
| 47_V | 142_T | 3.721 | 1.00 |
| 45_M | 98_R | 3.291 | 1.00 |
| 116_W | 153_S | 3.239 | 1.00 |
| 141_P | 147_V | 2.750 | 1.00 |
| 49_G | 96_V | 2.385 | 1.00 |
| 74_A | 96_V | 2.373 | 1.00 |
| 50_M | 56_A | 2.354 | 1.00 |
| 154_K | 173_I | 2.311 | 1.00 |
| 70_Q | 179_F | 2.306 | 1.00 |
| 124_G | 170_T | 2.294 | 1.00 |
| 89_G | 134_Q | 2.288 | 1.00 |
| 63_L | 114_V | 2.286 | 1.00 |
| 48_F | 111_L | 2.146 | 1.00 |
| 75_G | 138_A | 2.099 | 1.00 |
| 44_Q | 143_S | 2.094 | 1.00 |
| 94_A | 136_R | 2.070 | 1.00 |
| 116_W | 154_K | 2.057 | 1.00 |
| 56_A | 118_N | 2.042 | 1.00 |
| 71_V | 187_Q | 2.030 | 1.00 |
| 47_V | 98_R | 2.016 | 1.00 |
| 29_H | 191_S | 1.985 | 1.00 |
| 141_P | 175_E | 1.942 | 1.00 |
| 63_L | 106_I | 1.929 | 1.00 |
| 94_A | 138_A | 1.902 | 1.00 |
| 78_T | 85_E | 1.881 | 1.00 |
| 139_I | 150_A | 1.879 | 1.00 |
| 109_E | 149_A | 1.830 | 1.00 |
| 43_T | 67_Y | 1.755 | 1.00 |
| 53_F | 73_F | 1.745 | 1.00 |
| 94_A | 174_R | 1.723 | 1.00 |
| 64_K | 105_H | 1.721 | 1.00 |
| 70_Q | 98_R | 1.716 | 1.00 |
| 74_A | 176_G | 1.686 | 1.00 |
| 144_A | 147_V | 1.660 | 1.00 |
| 70_Q | 181_Y | 1.641 | 1.00 |
| 44_Q | 101_F | 1.625 | 1.00 |
| 44_Q | 146_H | 1.620 | 1.00 |
| 47_V | 96_V | 1.601 | 1.00 |
| 49_G | 138_A | 1.568 | 1.00 |
| 148_G | 152_K | 1.557 | 1.00 |
| 70_Q | 100_V | 1.514 | 1.00 |
| 119_H | 137_S | 1.499 | 1.00 |
| 82_T | 85_E | 1.480 | 1.00 |
| 107_S | 110_E | 1.474 | 1.00 |
| 47_V | 74_A | 1.445 | 1.00 |
| 126_R | 131_H | 1.432 | 1.00 |
| 55_G | 190_L | 1.409 | 1.00 |
| 184_D | 192_K | 1.382 | 0.99 |
| 112_L | 149_A | 1.365 | 0.99 |
| 155_E | 159_K | 1.358 | 0.99 |
| 61_W | 69_T | 1.353 | 0.99 |
| 61_W | 191_S | 1.343 | 0.99 |
| 109_E | 152_K | 1.331 | 0.99 |
| 50_M | 118_N | 1.319 | 0.99 |
| 123_Q | 126_R | 1.318 | 0.99 |
| 152_K | 156_D | 1.306 | 0.99 |
| 76_G | 93_H | 1.295 | 0.99 |
| 61_W | 188_Q | 1.280 | 0.99 |
| 142_T | 146_H | 1.270 | 0.99 |
| 102_Q | 105_H | 1.269 | 0.99 |
| 140_Y | 172_D | 1.260 | 0.99 |
| 59_K | 118_N | 1.248 | 0.99 |
| 137_S | 171_T | 1.244 | 0.98 |
| 84_K | 185_Y | 1.244 | 0.98 |
| 48_F | 112_L | 1.236 | 0.98 |
| 45_M | 100_V | 1.235 | 0.98 |
| 92_G | 133_S | 1.222 | 0.98 |
| 87_C | 134_Q | 1.208 | 0.98 |
| 48_F | 60_F | 1.188 | 0.98 |
| 74_A | 177_Q | 1.186 | 0.98 |
| 138_A | 174_R | 1.177 | 0.98 |
| 141_P | 173_I | 1.175 | 0.98 |
| 48_F | 108_F | 1.163 | 0.97 |
| 86_V | 91_T | 1.160 | 0.97 |
| 110_E | 113_K | 1.152 | 0.97 |
| 136_R | 172_D | 1.122 | 0.97 |
| 138_A | 172_D | 1.086 | 0.96 |
| 145_E | 148_G | 1.077 | 0.95 |
| 73_F | 183_E | 1.045 | 0.94 |
| 144_A | 148_G | 1.044 | 0.94 |
| 101_F | 146_H | 1.037 | 0.94 |
| 68_S | 100_V | 1.011 | 0.93 |
| 44_Q | 103_P | 1.002 | 0.92 |
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 | |
| 1ff3A | 3 | 0.9849 | 100 | 0.05 | Contact Map |
| 1fvgA | 1 | 0.9648 | 100 | 0.057 | Contact Map |
| 4d7lA | 3 | 0.9648 | 100 | 0.065 | Contact Map |
| 3bqhA | 1 | 0.7688 | 100 | 0.151 | Contact Map |
| 2j89A | 1 | 0.8392 | 100 | 0.162 | Contact Map |
| 3pimA | 3 | 0.8191 | 100 | 0.166 | Contact Map |
| 3e0mA | 4 | 0.7638 | 100 | 0.167 | Contact Map |
| 1nwaA | 1 | 0.7839 | 100 | 0.201 | Contact Map |
| 4gwbA | 1 | 0.7588 | 100 | 0.208 | Contact Map |
| 4lwlA | 1 | 0.7236 | 100 | 0.259 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)