| Tommy tutorial HA fragment |
| ID: | 1475692389 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (127) | ||
| Sequences: | 200 (39.2) | ||
| Seq/Len: | 1.575 | ||
| Nf(neff/√len): | 3.5 |
HHblits Results: (2016_02)
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: 1.575).
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_L | 66_S | 1.831 | 0.96 |
| 54_F | 123_S | 1.739 | 0.95 |
| 112_K | 115_S | 1.660 | 0.93 |
| 34_S | 74_E | 1.633 | 0.92 |
| 41_T | 44_S | 1.626 | 0.92 |
| 56_D | 64_L | 1.618 | 0.92 |
| 34_S | 73_F | 1.605 | 0.91 |
| 39_V | 66_S | 1.535 | 0.89 |
| 76_F | 97_Y | 1.464 | 0.85 |
| 23_N | 37_Y | 1.463 | 0.85 |
| 87_T | 114_G | 1.457 | 0.85 |
| 111_T | 115_S | 1.453 | 0.85 |
| 21_L | 90_G | 1.451 | 0.85 |
| 49_C | 103_F | 1.445 | 0.84 |
| 82_W | 117_Y | 1.431 | 0.84 |
| 61_R | 77_P | 1.416 | 0.83 |
| 89_K | 97_Y | 1.410 | 0.82 |
| 61_R | 78_K | 1.389 | 0.81 |
| 34_S | 92_T | 1.374 | 0.80 |
| 18_G | 52_G | 1.353 | 0.78 |
| 36_S | 59_E | 1.344 | 0.78 |
| 52_G | 58_E | 1.325 | 0.76 |
| 57_Y | 71_E | 1.297 | 0.74 |
| 101_S | 115_S | 1.293 | 0.74 |
| 80_S | 97_Y | 1.285 | 0.73 |
| 18_G | 58_E | 1.280 | 0.73 |
| 44_S | 85_H | 1.269 | 0.72 |
| 21_L | 71_E | 1.267 | 0.72 |
| 27_D | 30_L | 1.232 | 0.69 |
| 50_Y | 103_F | 1.224 | 0.68 |
| 11_L | 52_G | 1.219 | 0.68 |
| 4_L | 85_H | 1.213 | 0.67 |
| 55_I | 61_R | 1.210 | 0.67 |
| 29_L | 73_F | 1.206 | 0.66 |
| 115_S | 119_K | 1.206 | 0.66 |
| 11_L | 30_L | 1.198 | 0.66 |
| 26_C | 95_C | 1.196 | 0.65 |
| 26_C | 90_G | 1.192 | 0.65 |
| 35_W | 82_W | 1.123 | 0.58 |
| 8_A | 73_F | 1.119 | 0.58 |
| 21_L | 26_C | 1.099 | 0.56 |
| 38_I | 58_E | 1.097 | 0.56 |
| 50_Y | 117_Y | 1.095 | 0.55 |
| 21_L | 104_Y | 1.085 | 0.54 |
| 99_G | 124_Y | 1.084 | 0.54 |
| 46_N | 75_I | 1.083 | 0.54 |
| 11_L | 18_G | 1.083 | 0.54 |
| 52_G | 124_Y | 1.082 | 0.54 |
| 23_N | 52_G | 1.065 | 0.52 |
| 23_N | 36_S | 1.062 | 0.52 |
| 16_I | 125_V | 1.061 | 0.52 |
| 37_Y | 59_E | 1.059 | 0.52 |
| 11_L | 58_E | 1.058 | 0.51 |
| 23_N | 47_G | 1.058 | 0.51 |
| 50_Y | 102_S | 1.049 | 0.51 |
| 98_A | 107_L | 1.044 | 0.50 |
| 90_G | 95_C | 1.040 | 0.50 |
| 15_N | 44_S | 1.037 | 0.49 |
| 42_S | 116_S | 1.032 | 0.49 |
| 32_A | 112_K | 1.030 | 0.49 |
| 59_E | 72_K | 1.028 | 0.48 |
| 92_T | 95_C | 1.015 | 0.47 |
| 6_G | 85_H | 1.014 | 0.47 |
| 1_L | 75_I | 1.013 | 0.47 |
| 91_V | 101_S | 1.012 | 0.47 |
| 88_T | 97_Y | 1.011 | 0.47 |
| 26_C | 51_P | 1.009 | 0.46 |
| 30_L | 52_G | 1.007 | 0.46 |
| 13_K | 116_S | 1.005 | 0.46 |
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 | |
| 4wsrA | 6 | 0.9921 | 100 | 0.059 | Contact Map |
| 2wr1A | 3 | 0.9843 | 100 | 0.06 | Contact Map |
| 4xkgA | 3 | 0.9921 | 100 | 0.06 | Contact Map |
| 3ku3A | 1 | 0.9843 | 100 | 0.061 | Contact Map |
| 4gxxA | 3 | 1 | 100 | 0.064 | Contact Map |
| 4lvhA | 4 | 0.9449 | 100 | 0.067 | Contact Map |
| 4fqiA | 1 | 0.9921 | 100 | 0.068 | Contact Map |
| 3uyxA | 2 | 0.9528 | 100 | 0.075 | Contact Map |
| 4f23A | 3 | 0.9764 | 100 | 0.08 | Contact Map |
| 4h32A | 6 | 0.9685 | 100 | 0.08 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)