| 3lhe |
| ID: | 1453737443 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 143 (140) | ||
| Sequences: | 7081 (5351.1) | ||
| Seq/Len: | 50.579 | ||
| Nf(neff/√len): | 452.3 |
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: 50.579).
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 |
| 99_P | 115_L | 3.492 | 1.00 |
| 103_E | 136_D | 3.256 | 1.00 |
| 25_I | 57_W | 2.666 | 1.00 |
| 12_K | 45_I | 2.646 | 1.00 |
| 39_K | 55_H | 2.521 | 1.00 |
| 10_E | 45_I | 2.476 | 1.00 |
| 100_D | 103_E | 2.467 | 1.00 |
| 41_I | 55_H | 2.443 | 1.00 |
| 98_R | 114_F | 2.430 | 1.00 |
| 93_R | 143_E | 2.235 | 1.00 |
| 18_I | 36_F | 1.982 | 1.00 |
| 53_M | 103_E | 1.922 | 1.00 |
| 18_I | 60_I | 1.900 | 1.00 |
| 97_I | 117_R | 1.881 | 1.00 |
| 15_E | 41_I | 1.875 | 1.00 |
| 95_K | 117_R | 1.862 | 1.00 |
| 117_R | 134_Y | 1.807 | 1.00 |
| 49_I | 141_T | 1.798 | 1.00 |
| 92_V | 120_Q | 1.776 | 1.00 |
| 15_E | 39_K | 1.756 | 1.00 |
| 77_S | 81_N | 1.750 | 1.00 |
| 19_V | 39_K | 1.744 | 1.00 |
| 95_K | 143_E | 1.718 | 1.00 |
| 11_S | 44_R | 1.714 | 1.00 |
| 35_D | 61_S | 1.627 | 1.00 |
| 20_G | 36_F | 1.578 | 1.00 |
| 115_L | 136_D | 1.528 | 1.00 |
| 17_T | 39_K | 1.521 | 1.00 |
| 96_G | 116_M | 1.459 | 1.00 |
| 22_D | 25_I | 1.459 | 1.00 |
| 110_T | 113_D | 1.435 | 1.00 |
| 10_E | 48_S | 1.425 | 1.00 |
| 41_I | 102_K | 1.424 | 1.00 |
| 56_T | 131_E | 1.422 | 1.00 |
| 21_A | 37_V | 1.403 | 0.99 |
| 121_V | 129_T | 1.367 | 0.99 |
| 7_S | 47_H | 1.359 | 0.99 |
| 85_L | 124_L | 1.346 | 0.99 |
| 99_P | 109_L | 1.345 | 0.99 |
| 14_I | 43_L | 1.342 | 0.99 |
| 32_S | 35_D | 1.333 | 0.99 |
| 36_F | 60_I | 1.319 | 0.99 |
| 124_L | 128_R | 1.266 | 0.99 |
| 12_K | 43_L | 1.266 | 0.99 |
| 97_I | 115_L | 1.255 | 0.99 |
| 109_L | 115_L | 1.244 | 0.98 |
| 97_I | 136_D | 1.240 | 0.98 |
| 104_K | 112_Q | 1.211 | 0.98 |
| 124_L | 130_F | 1.199 | 0.98 |
| 52_I | 135_A | 1.186 | 0.98 |
| 80_Q | 86_Q | 1.175 | 0.98 |
| 119_E | 134_Y | 1.164 | 0.97 |
| 97_I | 103_E | 1.162 | 0.97 |
| 16_F | 38_Y | 1.160 | 0.97 |
| 43_L | 50_P | 1.154 | 0.97 |
| 19_V | 25_I | 1.154 | 0.97 |
| 78_H | 83_L | 1.144 | 0.97 |
| 98_R | 113_D | 1.135 | 0.97 |
| 52_I | 137_H | 1.129 | 0.97 |
| 76_Y | 122_A | 1.126 | 0.97 |
| 18_I | 38_Y | 1.107 | 0.96 |
| 86_Q | 125_T | 1.106 | 0.96 |
| 53_M | 106_F | 1.096 | 0.96 |
| 120_Q | 133_S | 1.092 | 0.96 |
| 39_K | 57_W | 1.084 | 0.96 |
| 138_L | 141_T | 1.070 | 0.95 |
| 44_R | 54_E | 1.065 | 0.95 |
| 41_I | 53_M | 1.053 | 0.95 |
| 99_P | 104_K | 1.040 | 0.94 |
| 21_A | 26_A | 1.036 | 0.94 |
| 113_D | 140_E | 1.035 | 0.94 |
| 76_Y | 131_E | 1.021 | 0.93 |
| 55_H | 134_Y | 1.001 | 0.92 |
| 26_A | 31_I | 1.001 | 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
- 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 | |
| 3lheA | 1 | 0.8671 | 99.9 | -0.049 | Contact Map |
| 2ikkA | 2 | 0.9301 | 99.9 | -0.037 | Contact Map |
| 2oggA | 1 | 0.9441 | 99.9 | -0.035 | Contact Map |
| 3ddvA | 4 | 0.972 | 99.9 | -0.026 | Contact Map |
| 2fa1A | 2 | 1 | 99.9 | -0.015 | Contact Map |
| 3cnvA | 4 | 1 | 99.9 | -0.014 | Contact Map |
| 3f8lA | 4 | 0.993 | 99.9 | -0.011 | Contact Map |
| 2p19A | 3 | 0.979 | 99.9 | -0.007 | Contact Map |
| 3hfiA | 1 | 0.9371 | 99.9 | -0.007 | Contact Map |
| 2pkhA | 8 | 0.9371 | 99.9 | 0.011 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)