| ompw |
| ID: | 1415239064 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 193 (190) | ||
| Sequences: | 2566 (1890.2) | ||
| Seq/Len: | 13.505 | ||
| Nf(neff/√len): | 137.1 |
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: 13.505).
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 |
| 154_G | 190_S | 3.402 | 1.00 |
| 156_F | 188_G | 3.293 | 1.00 |
| 108_F | 145_F | 3.134 | 1.00 |
| 159_V | 183_F | 3.125 | 1.00 |
| 23_Q | 57_E | 2.937 | 1.00 |
| 148_A | 151_K | 2.894 | 1.00 |
| 116_A | 135_F | 2.600 | 1.00 |
| 153_W | 191_Y | 2.591 | 1.00 |
| 148_A | 153_W | 2.569 | 1.00 |
| 161_Y | 183_F | 2.541 | 1.00 |
| 147_P | 155_V | 2.539 | 1.00 |
| 27_G | 53_T | 2.360 | 1.00 |
| 108_F | 143_F | 2.129 | 1.00 |
| 25_K | 55_S | 2.124 | 1.00 |
| 22_W | 58_Y | 2.114 | 1.00 |
| 22_W | 56_V | 2.046 | 1.00 |
| 153_W | 189_Y | 1.968 | 1.00 |
| 55_S | 190_S | 1.959 | 1.00 |
| 148_A | 152_N | 1.896 | 1.00 |
| 30_V | 48_H | 1.880 | 1.00 |
| 60_F | 67_A | 1.795 | 1.00 |
| 27_G | 55_S | 1.783 | 1.00 |
| 95_T | 138_A | 1.719 | 1.00 |
| 111_Y | 158_D | 1.717 | 1.00 |
| 59_F | 66_S | 1.693 | 1.00 |
| 69_L | 96_I | 1.684 | 1.00 |
| 113_G | 140_Q | 1.660 | 1.00 |
| 95_T | 113_G | 1.645 | 1.00 |
| 28_G | 50_Y | 1.624 | 1.00 |
| 107_R | 146_Q | 1.593 | 1.00 |
| 111_Y | 156_F | 1.547 | 1.00 |
| 113_G | 160_R | 1.546 | 1.00 |
| 107_R | 145_F | 1.521 | 1.00 |
| 152_N | 191_Y | 1.514 | 1.00 |
| 55_S | 68_E | 1.508 | 1.00 |
| 156_F | 190_S | 1.499 | 1.00 |
| 71_L | 92_L | 1.468 | 1.00 |
| 154_G | 192_K | 1.466 | 1.00 |
| 66_S | 101_H | 1.462 | 1.00 |
| 29_S | 51_A | 1.431 | 1.00 |
| 144_N | 190_S | 1.425 | 1.00 |
| 144_N | 154_G | 1.408 | 1.00 |
| 97_T | 101_H | 1.386 | 0.99 |
| 115_G | 138_A | 1.382 | 0.99 |
| 66_S | 99_K | 1.378 | 0.99 |
| 66_S | 70_L | 1.373 | 0.99 |
| 147_P | 189_Y | 1.368 | 0.99 |
| 53_T | 72_A | 1.363 | 0.99 |
| 157_V | 187_L | 1.359 | 0.99 |
| 144_N | 156_F | 1.342 | 0.99 |
| 29_S | 186_T | 1.336 | 0.99 |
| 57_E | 99_K | 1.330 | 0.99 |
| 117_T | 136_G | 1.300 | 0.99 |
| 55_S | 156_F | 1.279 | 0.99 |
| 32_A | 185_Y | 1.263 | 0.99 |
| 27_G | 188_G | 1.212 | 0.98 |
| 139_G | 161_Y | 1.200 | 0.98 |
| 111_Y | 140_Q | 1.189 | 0.98 |
| 97_T | 138_A | 1.188 | 0.98 |
| 65_F | 98_A | 1.176 | 0.98 |
| 113_G | 158_D | 1.157 | 0.97 |
| 92_L | 95_T | 1.156 | 0.97 |
| 61_G | 65_F | 1.119 | 0.96 |
| 68_E | 115_G | 1.112 | 0.96 |
| 70_L | 97_T | 1.098 | 0.96 |
| 21_N | 109_T | 1.073 | 0.95 |
| 27_G | 72_A | 1.071 | 0.95 |
| 25_K | 190_S | 1.068 | 0.95 |
| 5_A | 8_I | 1.067 | 0.95 |
| 160_R | 186_T | 1.061 | 0.95 |
| 68_E | 99_K | 1.055 | 0.95 |
| 59_F | 101_H | 1.042 | 0.94 |
| 74_P | 91_Q | 1.037 | 0.94 |
| 119_F | 164_I | 1.035 | 0.94 |
| 55_S | 70_L | 1.030 | 0.94 |
| 159_V | 185_Y | 1.030 | 0.94 |
| 163_D | 166_P | 1.029 | 0.94 |
| 34_S | 161_Y | 1.024 | 0.93 |
| 23_Q | 59_F | 1.024 | 0.93 |
| 70_L | 113_G | 1.017 | 0.93 |
| 158_D | 186_T | 1.016 | 0.93 |
| 137_V | 163_D | 1.013 | 0.93 |
| 109_T | 146_Q | 1.012 | 0.93 |
| 11_M | 15_S | 1.011 | 0.93 |
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 | |
| 2x27X | 1 | 0.9223 | 99.9 | 0.332 | Contact Map |
| 2f1vA | 6 | 0.8653 | 99.9 | 0.334 | Contact Map |
| 2mlhA | 1 | 0.8653 | 99.9 | 0.384 | Contact Map |
| 2k0lA | 1 | 0.9275 | 99.8 | 0.393 | Contact Map |
| 3nb3A | 3 | 0.6839 | 99.8 | 0.398 | Contact Map |
| 2lhfA | 1 | 0.8497 | 99.8 | 0.428 | Contact Map |
| 1qjpA | 1 | 0.6995 | 99.8 | 0.437 | Contact Map |
| 1p4tA | 1 | 0.7979 | 99.8 | 0.437 | Contact Map |
| 2jmmA | 1 | 0.7358 | 99.8 | 0.448 | Contact Map |
| 3qraA | 1 | 0.772 | 99.6 | 0.519 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)