| 3RLB |
| ID: | 1448278728 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 192 (178) | ||
| Sequences: | 498 (406.4) | ||
| Seq/Len: | 2.798 | ||
| Nf(neff/√len): | 30.5 |
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: 2.798).
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 |
| 24_I | 57_L | 3.166 | 1.00 |
| 23_E | 60_R | 2.781 | 1.00 |
| 128_V | 169_A | 2.750 | 1.00 |
| 58_S | 105_A | 2.418 | 1.00 |
| 57_L | 69_G | 2.414 | 1.00 |
| 132_Y | 136_F | 2.309 | 1.00 |
| 90_Q | 142_F | 2.159 | 1.00 |
| 71_L | 100_V | 2.115 | 1.00 |
| 99_P | 131_K | 2.083 | 1.00 |
| 18_V | 22_T | 2.082 | 1.00 |
| 23_E | 61_R | 1.959 | 0.99 |
| 136_F | 158_L | 1.838 | 0.99 |
| 160_V | 164_S | 1.778 | 0.99 |
| 104_I | 130_L | 1.754 | 0.99 |
| 34_I | 53_P | 1.726 | 0.98 |
| 108_F | 126_V | 1.682 | 0.98 |
| 63_L | 67_L | 1.623 | 0.97 |
| 168_T | 172_A | 1.575 | 0.97 |
| 44_W | 160_V | 1.568 | 0.96 |
| 136_F | 154_V | 1.562 | 0.96 |
| 63_L | 107_L | 1.535 | 0.96 |
| 28_A | 72_I | 1.524 | 0.96 |
| 59_L | 123_G | 1.478 | 0.95 |
| 74_G | 100_V | 1.471 | 0.94 |
| 20_L | 61_R | 1.463 | 0.94 |
| 51_C | 131_K | 1.462 | 0.94 |
| 125_F | 169_A | 1.444 | 0.94 |
| 144_S | 147_A | 1.408 | 0.92 |
| 67_L | 100_V | 1.405 | 0.92 |
| 132_Y | 163_I | 1.395 | 0.92 |
| 20_L | 65_A | 1.376 | 0.91 |
| 45_I | 160_V | 1.348 | 0.90 |
| 78_M | 91_A | 1.345 | 0.90 |
| 24_I | 72_I | 1.339 | 0.90 |
| 97_V | 134_F | 1.325 | 0.89 |
| 107_L | 126_V | 1.325 | 0.89 |
| 45_I | 94_E | 1.313 | 0.88 |
| 133_F | 136_F | 1.305 | 0.88 |
| 55_L | 172_A | 1.292 | 0.87 |
| 169_A | 173_F | 1.291 | 0.87 |
| 140_I | 154_V | 1.288 | 0.87 |
| 98_A | 135_H | 1.281 | 0.87 |
| 151_W | 159_A | 1.269 | 0.86 |
| 32_F | 80_T | 1.262 | 0.86 |
| 162_G | 166_I | 1.255 | 0.85 |
| 101_S | 134_F | 1.234 | 0.84 |
| 46_I | 131_K | 1.225 | 0.83 |
| 43_G | 143_W | 1.219 | 0.83 |
| 155_A | 159_A | 1.206 | 0.82 |
| 94_E | 160_V | 1.196 | 0.81 |
| 94_E | 164_S | 1.190 | 0.81 |
| 148_W | 151_W | 1.179 | 0.80 |
| 94_E | 138_A | 1.177 | 0.80 |
| 143_W | 147_A | 1.176 | 0.80 |
| 144_S | 157_S | 1.172 | 0.79 |
| 137_I | 141_I | 1.168 | 0.79 |
| 137_I | 154_V | 1.166 | 0.79 |
| 85_I | 91_A | 1.164 | 0.79 |
| 158_L | 162_G | 1.157 | 0.78 |
| 44_W | 94_E | 1.153 | 0.78 |
| 55_L | 124_T | 1.150 | 0.78 |
| 90_Q | 96_L | 1.128 | 0.76 |
| 45_I | 164_S | 1.128 | 0.76 |
| 38_P | 41_V | 1.123 | 0.75 |
| 78_M | 85_I | 1.110 | 0.74 |
| 122_L | 126_V | 1.110 | 0.74 |
| 140_I | 152_G | 1.104 | 0.73 |
| 42_Y | 163_I | 1.103 | 0.73 |
| 163_I | 167_L | 1.103 | 0.73 |
| 71_L | 74_G | 1.100 | 0.73 |
| 44_W | 164_S | 1.098 | 0.73 |
| 133_F | 137_I | 1.091 | 0.72 |
| 62_G | 66_G | 1.080 | 0.71 |
| 20_L | 24_I | 1.079 | 0.71 |
| 147_A | 157_S | 1.072 | 0.70 |
| 86_L | 91_A | 1.072 | 0.70 |
| 125_F | 154_V | 1.064 | 0.70 |
| 67_L | 71_L | 1.057 | 0.69 |
| 155_A | 158_L | 1.048 | 0.68 |
| 109_R | 113_A | 1.046 | 0.68 |
| 44_W | 156_Y | 1.046 | 0.68 |
| 24_I | 65_A | 1.040 | 0.67 |
| 145_Q | 150_G | 1.040 | 0.67 |
| 136_F | 157_S | 1.038 | 0.67 |
| 138_A | 143_W | 1.029 | 0.66 |
| 139_G | 157_S | 1.023 | 0.65 |
| 104_I | 178_I | 1.007 | 0.63 |
| 147_A | 150_G | 1.001 | 0.63 |
| 55_L | 59_L | 1.000 | 0.63 |
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 | |
| 3rlbA | 2 | 0.9219 | 100 | 0.507 | Contact Map |
| 4tkrA | 2 | 0.9271 | 99.9 | 0.524 | Contact Map |
| 4rfsS | 1 | 0.8906 | 99.8 | 0.648 | Contact Map |
| 3p5nA | 2 | 0.8385 | 99.5 | 0.71 | Contact Map |
| 4z7fA | 6 | 0 | 99.4 | 0.734 | Contact Map |
| 4hzuS | 1 | 0.8438 | 99.3 | 0.746 | Contact Map |
| 4huqS | 1 | 0.8438 | 99.1 | 0.766 | Contact Map |
| 4dveA | 3 | 0.9062 | 98.7 | 0.8 | Contact Map |
| 2ksfA | 1 | 0.5469 | 67.2 | 0.924 | Contact Map |
| 4m5bA | 1 | 0.9167 | 48.9 | 0.932 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)