| PilE |
| ID: | 1513726180 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 129 (118) | ||
| Sequences: | 1843 (1237.2) | ||
| Seq/Len: | 15.619 | ||
| Nf(neff/√len): | 113.9 |
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: 15.619).
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 |
| 50_D | 91_Q | 3.463 | 1.00 |
| 62_A | 85_D | 3.420 | 1.00 |
| 67_D | 83_Y | 3.088 | 1.00 |
| 89_T | 97_G | 2.682 | 1.00 |
| 42_L | 46_K | 2.457 | 1.00 |
| 119_T | 123_V | 2.252 | 1.00 |
| 99_V | 112_S | 2.225 | 1.00 |
| 64_Y | 70_D | 2.015 | 1.00 |
| 94_K | 117_G | 2.015 | 1.00 |
| 49_A | 53_T | 1.895 | 1.00 |
| 104_T | 109_V | 1.890 | 1.00 |
| 25_A | 28_G | 1.846 | 1.00 |
| 73_V | 77_K | 1.815 | 1.00 |
| 99_V | 111_V | 1.795 | 1.00 |
| 100_I | 108_V | 1.749 | 1.00 |
| 41_T | 44_Q | 1.720 | 1.00 |
| 76_T | 80_Q | 1.643 | 1.00 |
| 55_Q | 59_E | 1.523 | 1.00 |
| 91_Q | 98_F | 1.513 | 1.00 |
| 99_V | 114_G | 1.501 | 1.00 |
| 61_A | 110_N | 1.488 | 1.00 |
| 53_T | 98_F | 1.487 | 1.00 |
| 99_V | 113_I | 1.461 | 1.00 |
| 60_A | 84_L | 1.408 | 1.00 |
| 37_R | 40_G | 1.399 | 0.99 |
| 54_A | 110_N | 1.331 | 0.99 |
| 105_T | 109_V | 1.282 | 0.99 |
| 58_A | 85_D | 1.276 | 0.99 |
| 43_N | 47_V | 1.261 | 0.99 |
| 15_F | 30_L | 1.248 | 0.99 |
| 102_V | 108_V | 1.230 | 0.98 |
| 55_Q | 58_A | 1.215 | 0.98 |
| 32_A | 36_P | 1.209 | 0.98 |
| 74_T | 77_K | 1.203 | 0.98 |
| 42_L | 45_A | 1.198 | 0.98 |
| 58_A | 62_A | 1.198 | 0.98 |
| 53_T | 57_I | 1.184 | 0.98 |
| 72_N | 90_P | 1.167 | 0.97 |
| 52_A | 56_T | 1.149 | 0.97 |
| 50_D | 92_S | 1.143 | 0.97 |
| 50_D | 54_A | 1.130 | 0.97 |
| 19_E | 23_V | 1.088 | 0.96 |
| 31_A | 35_V | 1.079 | 0.95 |
| 16_T | 22_V | 1.059 | 0.95 |
| 48_N | 51_K | 1.057 | 0.95 |
| 57_I | 111_V | 1.053 | 0.95 |
| 20_L | 24_I | 1.050 | 0.94 |
| 61_A | 71_T | 1.048 | 0.94 |
| 43_N | 46_K | 1.046 | 0.94 |
| 47_V | 113_I | 1.032 | 0.94 |
| 33_I | 45_A | 1.008 | 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
- 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 | |
| 3g20A | 2 | 0.7287 | 99.7 | 0.49 | Contact Map |
| 3sokA | 2 | 0.876 | 99.6 | 0.515 | Contact Map |
| 2hi2A | 1 | 0.8682 | 99.6 | 0.527 | Contact Map |
| 1t92A | 2 | 0.6667 | 99.6 | 0.542 | Contact Map |
| 3gn9A | 3 | 0.6822 | 99.5 | 0.552 | Contact Map |
| 2kepA | 1 | 0.6899 | 99.5 | 0.56 | Contact Map |
| 2m7gA | 1 | 0.4729 | 99.3 | 0.597 | Contact Map |
| 1oqwA | 2 | 0.876 | 99.2 | 0.615 | Contact Map |
| 4noaA | 1 | 0.6202 | 70.3 | 0.88 | Contact Map |
| 4d40A | 2 | 0 | 54.7 | 0.891 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)