| 1CJWA |
| ID: | 1440458973 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 166 (150) | ||
| Sequences: | 5806 (4191.4) | ||
| Seq/Len: | 38.707 | ||
| Nf(neff/√len): | 342.2 |
HHblits Results: (2015_06)
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: 38.707).
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 |
| 9_R | 15_D | 3.237 | 1.00 |
| 55_W | 106_K | 3.142 | 1.00 |
| 108_S | 141_R | 3.012 | 1.00 |
| 17_A | 38_L | 2.912 | 1.00 |
| 115_L | 144_F | 2.902 | 1.00 |
| 25_E | 98_H | 2.530 | 1.00 |
| 9_R | 56_F | 2.504 | 1.00 |
| 115_L | 164_C | 2.428 | 1.00 |
| 62_V | 101_F | 2.376 | 1.00 |
| 65_I | 114_Y | 2.359 | 1.00 |
| 54_G | 61_L | 2.227 | 1.00 |
| 115_L | 127_A | 2.221 | 1.00 |
| 113_R | 116_H | 2.181 | 1.00 |
| 11_L | 19_V | 2.101 | 1.00 |
| 108_S | 142_F | 2.098 | 1.00 |
| 140_Q | 146_P | 2.094 | 1.00 |
| 25_E | 99_R | 2.004 | 1.00 |
| 137_P | 140_Q | 1.971 | 1.00 |
| 53_L | 113_R | 1.935 | 1.00 |
| 38_L | 42_Q | 1.928 | 1.00 |
| 63_A | 97_V | 1.884 | 1.00 |
| 146_P | 160_T | 1.853 | 1.00 |
| 126_R | 163_H | 1.839 | 1.00 |
| 112_W | 142_F | 1.828 | 1.00 |
| 101_F | 104_Q | 1.814 | 1.00 |
| 146_P | 149_P | 1.801 | 1.00 |
| 11_L | 54_G | 1.793 | 1.00 |
| 133_D | 158_T | 1.770 | 1.00 |
| 111_L | 142_F | 1.727 | 1.00 |
| 67_G | 114_Y | 1.676 | 1.00 |
| 136_V | 140_Q | 1.666 | 1.00 |
| 133_D | 160_T | 1.642 | 1.00 |
| 26_A | 96_A | 1.615 | 1.00 |
| 97_V | 106_K | 1.610 | 1.00 |
| 18_G | 21_E | 1.582 | 1.00 |
| 52_S | 66_I | 1.531 | 1.00 |
| 26_A | 102_R | 1.402 | 0.99 |
| 149_P | 158_T | 1.376 | 0.99 |
| 60_R | 100_S | 1.341 | 0.99 |
| 56_F | 59_G | 1.324 | 0.99 |
| 13_P | 46_T | 1.318 | 0.99 |
| 20_F | 24_R | 1.292 | 0.99 |
| 89_S | 126_R | 1.289 | 0.99 |
| 147_A | 161_E | 1.273 | 0.99 |
| 147_A | 163_H | 1.259 | 0.99 |
| 133_D | 149_P | 1.221 | 0.98 |
| 37_N | 40_E | 1.213 | 0.98 |
| 153_V | 159_F | 1.212 | 0.98 |
| 127_A | 144_F | 1.203 | 0.98 |
| 105_G | 108_S | 1.198 | 0.98 |
| 108_S | 112_W | 1.188 | 0.98 |
| 6_N | 55_W | 1.186 | 0.98 |
| 13_P | 42_Q | 1.184 | 0.98 |
| 128_V | 163_H | 1.171 | 0.98 |
| 117_H | 120_A | 1.161 | 0.97 |
| 65_I | 92_L | 1.161 | 0.97 |
| 53_L | 117_H | 1.149 | 0.97 |
| 88_H | 125_R | 1.133 | 0.97 |
| 60_R | 98_H | 1.115 | 0.96 |
| 42_Q | 46_T | 1.105 | 0.96 |
| 69_L | 124_V | 1.098 | 0.96 |
| 134_A | 157_L | 1.090 | 0.96 |
| 18_G | 61_L | 1.089 | 0.96 |
| 149_P | 160_T | 1.085 | 0.96 |
| 8_F | 53_L | 1.082 | 0.96 |
| 91_H | 128_V | 1.057 | 0.95 |
| 65_I | 110_L | 1.055 | 0.95 |
| 116_H | 120_A | 1.055 | 0.95 |
| 39_D | 43_H | 1.015 | 0.93 |
| 118_V | 127_A | 1.009 | 0.93 |
| 117_H | 121_Q | 1.005 | 0.93 |
| 56_F | 61_L | 1.000 | 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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 1cjwA | 1 | 0.994 | 99.9 | 0.252 | Contact Map |
| 1kuxA | 1 | 0.994 | 99.9 | 0.263 | Contact Map |
| 2reeA | 2 | 0.9578 | 99.9 | 0.295 | Contact Map |
| 4kvxA | 2 | 0.8675 | 99.9 | 0.351 | Contact Map |
| 2ob0A | 3 | 0.8855 | 99.9 | 0.351 | Contact Map |
| 2j8mA | 2 | 0.9036 | 99.9 | 0.358 | Contact Map |
| 3dr6A | 3 | 0.9036 | 99.9 | 0.36 | Contact Map |
| 2r7hA | 2 | 0.8916 | 99.9 | 0.365 | Contact Map |
| 4zbgA | 1 | 0 | 99.8 | 0.369 | Contact Map |
| 1n71A | 4 | 0.8614 | 99.8 | 0.371 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)