| sumo |
| ID: | 1438943209 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 158 (152) | ||
| Sequences: | 2499 (1587.7) | ||
| Seq/Len: | 16.441 | ||
| Nf(neff/√len): | 128.8 |
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: 16.441).
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 |
| 67_D | 71_S | 3.573 | 1.00 |
| 140_N | 143_E | 3.348 | 1.00 |
| 141_R | 145_E | 3.258 | 1.00 |
| 82_F | 136_I | 2.932 | 1.00 |
| 135_T | 139_Q | 2.750 | 1.00 |
| 130_Q | 133_A | 2.720 | 1.00 |
| 8_R | 12_E | 2.585 | 1.00 |
| 58_F | 152_A | 2.414 | 1.00 |
| 143_E | 146_K | 2.310 | 1.00 |
| 47_G | 51_T | 2.212 | 1.00 |
| 47_G | 54_E | 2.169 | 1.00 |
| 137_Y | 141_R | 2.121 | 1.00 |
| 64_F | 109_I | 2.121 | 1.00 |
| 37_N | 40_N | 2.072 | 1.00 |
| 5_A | 39_M | 1.944 | 1.00 |
| 75_C | 116_I | 1.903 | 1.00 |
| 40_N | 61_R | 1.901 | 1.00 |
| 42_E | 59_K | 1.877 | 1.00 |
| 128_P | 134_Y | 1.775 | 1.00 |
| 126_Q | 138_C | 1.747 | 1.00 |
| 84_P | 144_Y | 1.679 | 1.00 |
| 40_N | 63_L | 1.639 | 1.00 |
| 62_M | 75_C | 1.600 | 1.00 |
| 61_R | 78_E | 1.598 | 1.00 |
| 142_V | 145_E | 1.583 | 1.00 |
| 144_Y | 148_V | 1.562 | 1.00 |
| 9_L | 64_F | 1.491 | 1.00 |
| 41_W | 64_F | 1.490 | 1.00 |
| 60_L | 116_I | 1.420 | 1.00 |
| 150_A | 154_K | 1.418 | 1.00 |
| 11_Q | 15_A | 1.416 | 1.00 |
| 75_C | 112_I | 1.357 | 0.99 |
| 85_N | 119_L | 1.347 | 0.99 |
| 118_E | 122_E | 1.344 | 0.99 |
| 43_C | 62_M | 1.337 | 0.99 |
| 54_E | 149_R | 1.332 | 0.99 |
| 82_F | 133_A | 1.274 | 0.99 |
| 152_A | 156_A | 1.264 | 0.99 |
| 52_P | 145_E | 1.251 | 0.99 |
| 61_R | 76_K | 1.227 | 0.98 |
| 143_E | 147_R | 1.226 | 0.98 |
| 87_Y | 91_T | 1.221 | 0.98 |
| 124_N | 127_D | 1.219 | 0.98 |
| 108_T | 111_Q | 1.209 | 0.98 |
| 60_L | 75_C | 1.208 | 0.98 |
| 145_E | 149_R | 1.203 | 0.98 |
| 151_Q | 155_F | 1.202 | 0.98 |
| 80_P | 155_F | 1.200 | 0.98 |
| 148_V | 152_A | 1.199 | 0.98 |
| 23_G | 117_Q | 1.197 | 0.98 |
| 95_S | 102_D | 1.195 | 0.98 |
| 95_S | 98_E | 1.191 | 0.98 |
| 29_T | 42_E | 1.187 | 0.98 |
| 104_R | 107_I | 1.160 | 0.97 |
| 85_N | 123_P | 1.159 | 0.97 |
| 29_T | 40_N | 1.159 | 0.97 |
| 90_G | 97_L | 1.127 | 0.97 |
| 148_V | 151_Q | 1.125 | 0.97 |
| 113_L | 117_Q | 1.116 | 0.96 |
| 125_I | 137_Y | 1.109 | 0.96 |
| 60_L | 77_F | 1.102 | 0.96 |
| 136_I | 147_R | 1.080 | 0.95 |
| 59_K | 78_E | 1.079 | 0.95 |
| 110_K | 114_L | 1.078 | 0.95 |
| 49_K | 54_E | 1.070 | 0.95 |
| 147_R | 151_Q | 1.056 | 0.95 |
| 87_Y | 129_A | 1.040 | 0.94 |
| 53_W | 69_P | 1.033 | 0.94 |
| 52_P | 152_A | 1.032 | 0.94 |
| 94_L | 98_E | 1.027 | 0.94 |
| 147_R | 150_A | 1.022 | 0.93 |
| 124_N | 129_A | 1.021 | 0.93 |
| 83_H | 86_V | 1.016 | 0.93 |
| 95_S | 107_I | 1.016 | 0.93 |
| 9_L | 41_W | 1.003 | 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
- 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 | |
| 3bzhA | 1 | 0.9494 | 100 | 0.045 | Contact Map |
| 2grrA | 1 | 0.9937 | 100 | 0.054 | Contact Map |
| 2gjdA | 4 | 0.9873 | 100 | 0.059 | Contact Map |
| 1ayzA | 3 | 0.9494 | 100 | 0.062 | Contact Map |
| 4l83A | 1 | 0.9873 | 100 | 0.063 | Contact Map |
| 3rczB | 1 | 0.981 | 100 | 0.066 | Contact Map |
| 2clwA | 1 | 0.943 | 100 | 0.069 | Contact Map |
| 4ddgA | 6 | 0.9494 | 100 | 0.069 | Contact Map |
| 4ladA | 1 | 0.962 | 100 | 0.07 | Contact Map |
| 4m1nA | 3 | 1 | 100 | 0.071 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)