| 4pgr |
| ID: | 1501760764 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 207 (203) | ||
| Sequences: | 924 (903.8) | ||
| Seq/Len: | 4.552 | ||
| Nf(neff/√len): | 63.4 |
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: 4.552).
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 |
| 12_L | 167_L | 3.732 | 1.00 |
| 121_W | 165_Y | 3.002 | 1.00 |
| 155_G | 197_N | 2.956 | 1.00 |
| 107_G | 167_L | 2.644 | 1.00 |
| 166_D | 190_D | 2.635 | 1.00 |
| 163_I | 194_L | 2.207 | 1.00 |
| 83_Y | 203_G | 2.130 | 1.00 |
| 42_I | 46_A | 2.113 | 1.00 |
| 107_G | 111_A | 2.089 | 1.00 |
| 103_F | 191_F | 2.010 | 1.00 |
| 124_L | 165_Y | 1.983 | 1.00 |
| 189_L | 193_N | 1.964 | 1.00 |
| 170_I | 187_L | 1.897 | 1.00 |
| 135_G | 151_Y | 1.864 | 1.00 |
| 131_L | 155_G | 1.840 | 1.00 |
| 22_A | 188_Y | 1.816 | 1.00 |
| 106_L | 164_L | 1.816 | 1.00 |
| 117_L | 164_L | 1.780 | 1.00 |
| 12_L | 107_G | 1.741 | 1.00 |
| 168_N | 172_H | 1.634 | 0.99 |
| 91_V | 202_F | 1.623 | 0.99 |
| 124_L | 161_L | 1.608 | 0.99 |
| 156_T | 194_L | 1.601 | 0.99 |
| 159_F | 193_N | 1.551 | 0.99 |
| 129_L | 133_V | 1.541 | 0.99 |
| 149_M | 201_F | 1.540 | 0.99 |
| 98_S | 202_F | 1.540 | 0.99 |
| 98_S | 198_L | 1.533 | 0.98 |
| 106_L | 160_S | 1.522 | 0.98 |
| 76_L | 196_I | 1.515 | 0.98 |
| 157_I | 161_L | 1.508 | 0.98 |
| 18_T | 65_V | 1.501 | 0.98 |
| 198_L | 202_F | 1.499 | 0.98 |
| 110_G | 168_N | 1.488 | 0.98 |
| 7_I | 11_I | 1.465 | 0.98 |
| 80_V | 92_V | 1.418 | 0.97 |
| 125_L | 129_L | 1.401 | 0.97 |
| 4_K | 7_I | 1.398 | 0.97 |
| 137_F | 141_S | 1.393 | 0.97 |
| 197_N | 200_R | 1.392 | 0.97 |
| 27_F | 31_F | 1.390 | 0.97 |
| 14_V | 18_T | 1.387 | 0.97 |
| 102_I | 198_L | 1.384 | 0.97 |
| 101_V | 133_V | 1.383 | 0.97 |
| 113_M | 168_N | 1.349 | 0.96 |
| 123_F | 127_A | 1.333 | 0.95 |
| 105_V | 129_L | 1.313 | 0.95 |
| 153_V | 157_I | 1.293 | 0.94 |
| 173_R | 183_M | 1.279 | 0.94 |
| 49_I | 53_W | 1.279 | 0.94 |
| 110_G | 118_S | 1.268 | 0.94 |
| 109_I | 113_M | 1.259 | 0.93 |
| 45_V | 48_I | 1.247 | 0.93 |
| 180_I | 183_M | 1.239 | 0.93 |
| 103_F | 163_I | 1.232 | 0.92 |
| 95_A | 198_L | 1.229 | 0.92 |
| 128_V | 132_A | 1.218 | 0.92 |
| 113_M | 117_L | 1.216 | 0.92 |
| 153_V | 201_F | 1.203 | 0.91 |
| 103_F | 187_L | 1.188 | 0.90 |
| 69_A | 73_G | 1.187 | 0.90 |
| 159_F | 162_Y | 1.163 | 0.89 |
| 79_I | 83_Y | 1.160 | 0.89 |
| 190_D | 195_F | 1.155 | 0.89 |
| 43_L | 48_I | 1.154 | 0.89 |
| 154_I | 158_V | 1.153 | 0.89 |
| 109_I | 112_K | 1.144 | 0.88 |
| 93_L | 97_G | 1.144 | 0.88 |
| 16_V | 104_A | 1.143 | 0.88 |
| 118_S | 168_N | 1.135 | 0.87 |
| 131_L | 158_V | 1.133 | 0.87 |
| 152_S | 197_N | 1.131 | 0.87 |
| 36_L | 39_P | 1.125 | 0.87 |
| 159_F | 189_L | 1.124 | 0.87 |
| 18_T | 69_A | 1.122 | 0.87 |
| 158_V | 161_L | 1.119 | 0.86 |
| 90_Y | 132_A | 1.116 | 0.86 |
| 129_L | 132_A | 1.115 | 0.86 |
| 146_A | 150_A | 1.092 | 0.85 |
| 159_F | 166_D | 1.089 | 0.84 |
| 94_E | 202_F | 1.083 | 0.84 |
| 67_T | 71_V | 1.081 | 0.84 |
| 14_V | 62_Y | 1.076 | 0.83 |
| 159_F | 190_D | 1.071 | 0.83 |
| 119_F | 123_F | 1.066 | 0.83 |
| 145_S | 148_M | 1.065 | 0.83 |
| 25_G | 70_F | 1.060 | 0.82 |
| 193_N | 196_I | 1.057 | 0.82 |
| 139_I | 157_I | 1.052 | 0.81 |
| 25_G | 29_G | 1.044 | 0.81 |
| 133_V | 137_F | 1.043 | 0.81 |
| 170_I | 186_S | 1.032 | 0.80 |
| 34_V | 38_L | 1.028 | 0.79 |
| 63_A | 67_T | 1.028 | 0.79 |
| 188_Y | 195_F | 1.021 | 0.79 |
| 109_I | 115_K | 1.020 | 0.79 |
| 96_F | 144_N | 1.010 | 0.78 |
| 166_D | 189_L | 1.004 | 0.77 |
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 | |
| 4pgrA | 1 | 0.9952 | 100 | 0.004 | Contact Map |
| 4i0uA | 10 | 0.2802 | 6.4 | 0.935 | Contact Map |
| 4ev6A | 5 | 0.2899 | 6.4 | 0.935 | Contact Map |
| 1r8hA | 6 | 0.1401 | 3.2 | 0.944 | Contact Map |
| 3w9iA | 6 | 0.7246 | 3.1 | 0.945 | Contact Map |
| 4dx5A | 3 | 0.7729 | 2.1 | 0.95 | Contact Map |
| 3ne5A | 1 | 0.7391 | 1.8 | 0.951 | Contact Map |
| 4b4aA | 1 | 0.6473 | 1.8 | 0.951 | Contact Map |
| 3j9pD | 4 | 0.8599 | 1.5 | 0.953 | Contact Map |
| 2xq2A | 1 | 0.7778 | 1.4 | 0.954 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)