| PilE Hbits |
| ID: | 1512760924 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 139 (139) | ||
| Sequences: | 1467 (1149.8) | ||
| Seq/Len: | 10.554 | ||
| Nf(neff/√len): | 97.5 |
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: 10.554).
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 |
| 119_T | 123_D | 3.947 | 1.00 |
| 32_E | 35_R | 3.449 | 1.00 |
| 38_K | 85_N | 3.190 | 1.00 |
| 56_F | 60_N | 2.895 | 1.00 |
| 48_S | 52_A | 2.743 | 1.00 |
| 104_R | 114_G | 2.623 | 1.00 |
| 113_C | 138_C | 2.521 | 1.00 |
| 46_L | 100_L | 2.199 | 1.00 |
| 27_Y | 31_T | 2.177 | 1.00 |
| 117_E | 125_A | 2.128 | 1.00 |
| 41_E | 45_A | 2.094 | 1.00 |
| 53_L | 57_Y | 1.996 | 1.00 |
| 39_R | 114_G | 1.981 | 1.00 |
| 89_A | 101_R | 1.886 | 1.00 |
| 50_A | 98_F | 1.854 | 1.00 |
| 87_Q | 105_T | 1.762 | 1.00 |
| 31_T | 35_R | 1.625 | 1.00 |
| 39_R | 86_Y | 1.612 | 1.00 |
| 98_F | 120_H | 1.605 | 1.00 |
| 33_S | 36_K | 1.568 | 1.00 |
| 89_A | 103_T | 1.512 | 1.00 |
| 97_T | 120_H | 1.488 | 1.00 |
| 39_R | 104_R | 1.473 | 1.00 |
| 2_K | 5_L | 1.468 | 1.00 |
| 94_S | 97_T | 1.388 | 0.99 |
| 46_L | 118_L | 1.364 | 0.99 |
| 53_L | 66_A | 1.349 | 0.99 |
| 38_K | 41_E | 1.346 | 0.99 |
| 39_R | 113_C | 1.302 | 0.99 |
| 16_V | 26_A | 1.288 | 0.99 |
| 15_V | 19_V | 1.286 | 0.99 |
| 67_D | 70_A | 1.277 | 0.99 |
| 101_R | 115_E | 1.267 | 0.99 |
| 1_M | 5_L | 1.262 | 0.99 |
| 6_G | 9_L | 1.256 | 0.99 |
| 126_L | 135_A | 1.246 | 0.98 |
| 41_E | 48_S | 1.233 | 0.98 |
| 13_M | 16_V | 1.230 | 0.98 |
| 30_Y | 34_V | 1.208 | 0.98 |
| 92_D | 97_T | 1.202 | 0.98 |
| 39_R | 110_S | 1.201 | 0.98 |
| 118_L | 125_A | 1.177 | 0.98 |
| 53_L | 67_D | 1.150 | 0.97 |
| 45_A | 49_G | 1.149 | 0.97 |
| 45_A | 88_I | 1.142 | 0.97 |
| 81_S | 84_A | 1.139 | 0.97 |
| 50_A | 118_L | 1.124 | 0.97 |
| 86_Y | 114_G | 1.117 | 0.96 |
| 7_F | 11_E | 1.105 | 0.96 |
| 54_E | 63_Y | 1.105 | 0.96 |
| 55_R | 58_S | 1.096 | 0.96 |
| 55_R | 61_N | 1.094 | 0.96 |
| 8_T | 12_L | 1.078 | 0.95 |
| 50_A | 122_G | 1.054 | 0.95 |
| 58_S | 61_N | 1.040 | 0.94 |
| 90_A | 98_F | 1.038 | 0.94 |
| 22_L | 30_Y | 1.037 | 0.94 |
| 46_L | 98_F | 1.037 | 0.94 |
| 17_A | 25_I | 1.032 | 0.94 |
| 99_T | 119_T | 1.029 | 0.94 |
| 113_C | 126_L | 1.028 | 0.94 |
| 103_T | 115_E | 1.022 | 0.93 |
| 91_V | 99_T | 1.008 | 0.93 |
| 40_A | 44_A | 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 | |
| 4noaA | 1 | 0.741 | 99.8 | 0.524 | Contact Map |
| 2m3kA | 1 | 0.705 | 99.8 | 0.527 | Contact Map |
| 4d40A | 2 | 0 | 99.7 | 0.543 | Contact Map |
| 3sokA | 2 | 0.9568 | 99.7 | 0.562 | Contact Map |
| 2hi2A | 1 | 0.9065 | 99.7 | 0.565 | Contact Map |
| 1oqwA | 2 | 0.9137 | 99.6 | 0.598 | Contact Map |
| 2m7gA | 1 | 0.4388 | 99.5 | 0.612 | Contact Map |
| 3g20A | 2 | 0.7554 | 98.7 | 0.734 | Contact Map |
| 1x6zA | 1 | 0.7338 | 95.4 | 0.843 | Contact Map |
| 2opeA | 4 | 0.7482 | 95.1 | 0.846 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)