| pmo-test mt03000 |
| ID: | 1414000918 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 238 (220) | ||
| Sequences: | 574 (470.2) | ||
| Seq/Len: | 2.609 | ||
| Nf(neff/√len): | 31.7 |
HHblits Results: (2013_03)
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: 2.609).
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 |
| 193_I | 196_Y | 3.610 | 1.00 |
| 61_A | 178_T | 3.462 | 1.00 |
| 150_N | 176_K | 3.219 | 1.00 |
| 10_A | 64_D | 3.214 | 1.00 |
| 59_E | 176_K | 2.875 | 1.00 |
| 148_P | 180_S | 2.862 | 1.00 |
| 84_M | 175_I | 2.801 | 1.00 |
| 84_M | 102_F | 2.720 | 1.00 |
| 87_C | 91_F | 2.711 | 1.00 |
| 61_A | 64_D | 2.627 | 1.00 |
| 145_G | 227_G | 2.376 | 1.00 |
| 146_L | 225_F | 2.238 | 1.00 |
| 102_F | 185_P | 2.160 | 1.00 |
| 40_S | 43_D | 2.006 | 0.99 |
| 198_Q | 201_D | 1.977 | 0.99 |
| 41_A | 168_F | 1.941 | 0.99 |
| 84_M | 177_V | 1.929 | 0.99 |
| 6_S | 13_D | 1.902 | 0.99 |
| 84_M | 104_I | 1.857 | 0.99 |
| 108_G | 219_I | 1.835 | 0.99 |
| 145_G | 225_F | 1.804 | 0.99 |
| 46_L | 193_I | 1.769 | 0.98 |
| 100_G | 192_A | 1.766 | 0.98 |
| 153_V | 175_I | 1.761 | 0.98 |
| 160_L | 163_A | 1.757 | 0.98 |
| 85_Y | 99_A | 1.754 | 0.98 |
| 81_L | 158_I | 1.744 | 0.98 |
| 59_E | 178_T | 1.729 | 0.98 |
| 84_M | 153_V | 1.693 | 0.98 |
| 47_R | 96_G | 1.683 | 0.98 |
| 106_E | 219_I | 1.679 | 0.98 |
| 183_A | 225_F | 1.676 | 0.97 |
| 142_I | 153_V | 1.641 | 0.97 |
| 158_I | 166_P | 1.624 | 0.97 |
| 206_F | 218_K | 1.624 | 0.97 |
| 46_L | 168_F | 1.596 | 0.96 |
| 191_A | 222_P | 1.587 | 0.96 |
| 62_P | 178_T | 1.527 | 0.95 |
| 65_T | 141_K | 1.472 | 0.94 |
| 80_I | 127_D | 1.469 | 0.94 |
| 152_L | 174_Q | 1.459 | 0.93 |
| 207_N | 210_D | 1.446 | 0.93 |
| 84_M | 142_I | 1.425 | 0.92 |
| 85_Y | 100_G | 1.418 | 0.92 |
| 82_V | 153_V | 1.387 | 0.91 |
| 81_L | 106_E | 1.364 | 0.90 |
| 65_T | 139_S | 1.349 | 0.89 |
| 202_P | 207_N | 1.347 | 0.89 |
| 104_I | 140_S | 1.331 | 0.88 |
| 62_P | 180_S | 1.326 | 0.88 |
| 146_L | 183_A | 1.315 | 0.87 |
| 192_A | 195_G | 1.304 | 0.87 |
| 77_Q | 129_A | 1.274 | 0.85 |
| 158_I | 204_I | 1.263 | 0.84 |
| 104_I | 153_V | 1.252 | 0.84 |
| 64_D | 144_D | 1.245 | 0.83 |
| 109_F | 124_S | 1.237 | 0.83 |
| 86_K | 147_A | 1.230 | 0.82 |
| 68_A | 82_V | 1.224 | 0.82 |
| 145_G | 183_A | 1.221 | 0.81 |
| 193_I | 197_C | 1.212 | 0.81 |
| 151_Y | 156_E | 1.185 | 0.79 |
| 67_T | 137_S | 1.178 | 0.78 |
| 191_A | 196_Y | 1.176 | 0.78 |
| 3_A | 35_Y | 1.171 | 0.78 |
| 83_W | 222_P | 1.167 | 0.77 |
| 85_Y | 94_C | 1.164 | 0.77 |
| 147_A | 184_E | 1.148 | 0.76 |
| 49_N | 171_E | 1.144 | 0.75 |
| 38_V | 66_I | 1.142 | 0.75 |
| 80_I | 131_L | 1.140 | 0.75 |
| 168_F | 204_I | 1.137 | 0.75 |
| 183_A | 187_A | 1.120 | 0.73 |
| 90_D | 150_N | 1.119 | 0.73 |
| 217_Y | 221_G | 1.114 | 0.72 |
| 106_E | 223_P | 1.111 | 0.72 |
| 45_K | 50_G | 1.108 | 0.72 |
| 35_Y | 171_E | 1.098 | 0.71 |
| 77_Q | 208_I | 1.093 | 0.70 |
| 105_D | 138_W | 1.090 | 0.70 |
| 57_Y | 92_S | 1.087 | 0.70 |
| 160_L | 166_P | 1.085 | 0.70 |
| 61_A | 179_G | 1.082 | 0.69 |
| 18_S | 25_Q | 1.081 | 0.69 |
| 60_A | 142_I | 1.078 | 0.69 |
| 34_D | 37_P | 1.076 | 0.69 |
| 99_A | 174_Q | 1.068 | 0.68 |
| 58_A | 70_W | 1.057 | 0.67 |
| 151_Y | 154_R | 1.055 | 0.66 |
| 149_G | 154_R | 1.050 | 0.66 |
| 203_N | 217_Y | 1.047 | 0.66 |
| 166_P | 204_I | 1.043 | 0.65 |
| 57_Y | 175_I | 1.040 | 0.65 |
| 70_W | 73_W | 1.039 | 0.65 |
| 91_F | 94_C | 1.038 | 0.65 |
| 30_W | 174_Q | 1.037 | 0.65 |
| 67_T | 139_S | 1.035 | 0.64 |
| 37_P | 49_N | 1.027 | 0.63 |
| 15_P | 18_S | 1.019 | 0.63 |
| 149_G | 156_E | 1.018 | 0.62 |
| 104_I | 142_I | 1.003 | 0.61 |
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 | |
| 4eisA | 1 | 0.8824 | 100 | 0.222 | Contact Map |
| 3zudA | 1 | 0.8992 | 100 | 0.231 | Contact Map |
| 4eirA | 2 | 0.8445 | 100 | 0.245 | Contact Map |
| 2vtcA | 2 | 0.8824 | 100 | 0.247 | Contact Map |
| 4b5qA | 2 | 0.8445 | 100 | 0.266 | Contact Map |
| 3ejaA | 4 | 0.8319 | 100 | 0.293 | Contact Map |
| 4maiA | 1 | 0.7479 | 100 | 0.436 | Contact Map |
| 2bemA | 3 | 0.6429 | 84.4 | 0.944 | Contact Map |
| 4oy7A | 8 | 0.584 | 83.6 | 0.944 | Contact Map |
| 2xwxA | 2 | 0.7479 | 60.8 | 0.954 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)