| E4 it1 |
| ID: | 1490239061 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 212 (208) | ||
| Sequences: | 760 (647.2) | ||
| Seq/Len: | 3.654 | ||
| Nf(neff/√len): | 44.9 |
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: 3.654).
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 |
| 64_W | 111_Y | 3.927 | 1.00 |
| 127_W | 131_V | 3.497 | 1.00 |
| 155_V | 159_I | 2.951 | 1.00 |
| 60_M | 116_L | 2.743 | 1.00 |
| 174_I | 178_G | 2.398 | 1.00 |
| 61_E | 65_A | 2.136 | 1.00 |
| 110_R | 118_G | 1.877 | 1.00 |
| 68_G | 72_F | 1.862 | 1.00 |
| 9_V | 12_G | 1.803 | 0.99 |
| 9_V | 13_I | 1.725 | 0.99 |
| 184_I | 187_Y | 1.676 | 0.99 |
| 187_Y | 191_L | 1.674 | 0.99 |
| 109_Q | 112_L | 1.662 | 0.99 |
| 8_R | 12_G | 1.617 | 0.98 |
| 64_W | 67_Y | 1.603 | 0.98 |
| 47_L | 80_S | 1.594 | 0.98 |
| 151_F | 155_V | 1.582 | 0.98 |
| 25_L | 28_H | 1.557 | 0.98 |
| 50_V | 73_A | 1.549 | 0.98 |
| 177_F | 187_Y | 1.518 | 0.97 |
| 89_L | 140_L | 1.512 | 0.97 |
| 32_L | 37_F | 1.496 | 0.97 |
| 23_L | 45_N | 1.484 | 0.97 |
| 71_D | 74_S | 1.480 | 0.97 |
| 71_D | 110_R | 1.472 | 0.97 |
| 182_E | 187_Y | 1.468 | 0.97 |
| 174_I | 177_F | 1.463 | 0.96 |
| 110_R | 119_C | 1.424 | 0.96 |
| 123_Q | 129_Y | 1.421 | 0.96 |
| 75_F | 79_F | 1.413 | 0.95 |
| 10_A | 14_L | 1.385 | 0.95 |
| 89_L | 93_R | 1.377 | 0.95 |
| 83_L | 87_C | 1.350 | 0.94 |
| 35_V | 39_L | 1.343 | 0.94 |
| 101_L | 104_A | 1.337 | 0.93 |
| 8_R | 59_N | 1.336 | 0.93 |
| 69_L | 73_A | 1.330 | 0.93 |
| 177_F | 182_E | 1.329 | 0.93 |
| 22_P | 45_N | 1.316 | 0.93 |
| 10_A | 13_I | 1.300 | 0.92 |
| 152_P | 178_G | 1.295 | 0.92 |
| 29_N | 37_F | 1.287 | 0.92 |
| 202_G | 206_S | 1.268 | 0.91 |
| 35_V | 90_A | 1.264 | 0.91 |
| 14_L | 18_L | 1.251 | 0.90 |
| 18_L | 48_T | 1.241 | 0.89 |
| 19_C | 52_A | 1.240 | 0.89 |
| 107_S | 194_P | 1.230 | 0.89 |
| 87_C | 92_M | 1.221 | 0.88 |
| 111_Y | 118_G | 1.221 | 0.88 |
| 194_P | 198_D | 1.218 | 0.88 |
| 86_T | 140_L | 1.207 | 0.88 |
| 151_F | 182_E | 1.204 | 0.87 |
| 112_L | 122_T | 1.201 | 0.87 |
| 183_A | 187_Y | 1.195 | 0.87 |
| 177_F | 183_A | 1.192 | 0.87 |
| 96_A | 102_L | 1.187 | 0.86 |
| 105_H | 187_Y | 1.168 | 0.85 |
| 76_A | 165_I | 1.161 | 0.85 |
| 18_L | 170_A | 1.139 | 0.83 |
| 81_F | 125_P | 1.139 | 0.83 |
| 100_N | 155_V | 1.137 | 0.83 |
| 5_L | 9_V | 1.118 | 0.82 |
| 180_T | 183_A | 1.114 | 0.81 |
| 201_F | 204_S | 1.095 | 0.80 |
| 33_A | 41_I | 1.094 | 0.80 |
| 79_F | 82_G | 1.091 | 0.79 |
| 174_I | 182_E | 1.090 | 0.79 |
| 152_P | 177_F | 1.089 | 0.79 |
| 203_S | 207_A | 1.086 | 0.79 |
| 13_I | 17_L | 1.083 | 0.79 |
| 194_P | 197_A | 1.078 | 0.78 |
| 65_A | 68_G | 1.076 | 0.78 |
| 178_G | 183_A | 1.075 | 0.78 |
| 54_I | 58_D | 1.075 | 0.78 |
| 113_I | 118_G | 1.071 | 0.78 |
| 46_I | 50_V | 1.067 | 0.77 |
| 43_F | 54_I | 1.061 | 0.77 |
| 30_H | 33_A | 1.061 | 0.77 |
| 11_L | 163_G | 1.057 | 0.76 |
| 178_G | 182_E | 1.055 | 0.76 |
| 71_D | 75_F | 1.054 | 0.76 |
| 138_L | 154_V | 1.053 | 0.76 |
| 34_A | 43_F | 1.050 | 0.76 |
| 186_D | 190_V | 1.050 | 0.76 |
| 164_W | 177_F | 1.043 | 0.75 |
| 12_G | 23_L | 1.043 | 0.75 |
| 12_G | 59_N | 1.039 | 0.75 |
| 88_M | 146_V | 1.033 | 0.74 |
| 199_G | 202_G | 1.031 | 0.74 |
| 202_G | 205_H | 1.029 | 0.74 |
| 70_C | 119_C | 1.029 | 0.74 |
| 108_A | 112_L | 1.014 | 0.72 |
| 26_L | 31_E | 1.012 | 0.72 |
| 34_A | 58_D | 1.011 | 0.72 |
| 195_G | 198_D | 1.011 | 0.72 |
| 198_D | 204_S | 1.007 | 0.71 |
| 11_L | 44_K | 1.005 | 0.71 |
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 | |
| 4xesA | 1 | 0 | 22.9 | 0.938 | Contact Map |
| 2z73A | 2 | 0.9623 | 22.5 | 0.938 | Contact Map |
| 4pxzA | 1 | 0.9104 | 21.4 | 0.938 | Contact Map |
| 4n6hA | 1 | 0.9434 | 20.3 | 0.939 | Contact Map |
| 3oduA | 2 | 0.9481 | 17.7 | 0.94 | Contact Map |
| 4grvA | 1 | 0.9434 | 12.7 | 0.944 | Contact Map |
| 4mbsA | 2 | 0.9623 | 12 | 0.945 | Contact Map |
| 4ea3A | 2 | 0.9434 | 11.8 | 0.945 | Contact Map |
| 4mqsA | 1 | 0.816 | 11.1 | 0.946 | Contact Map |
| 3emlA | 1 | 0.9481 | 9.4 | 0.948 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)