| flip_salmonella_withoutsignal |
| ID: | 1446547013 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 224 (207) | ||
| Sequences: | 1396 (745.4) | ||
| Seq/Len: | 6.744 | ||
| Nf(neff/√len): | 51.8 |
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: 6.744).
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 |
| 87_I | 113_L | 4.364 | 1.00 |
| 86_K | 90_D | 3.126 | 1.00 |
| 88_Y | 93_Q | 3.024 | 1.00 |
| 101_S | 104_E | 2.507 | 1.00 |
| 47_I | 68_L | 2.507 | 1.00 |
| 110_A | 146_M | 2.457 | 1.00 |
| 100_I | 108_K | 2.414 | 1.00 |
| 46_I | 50_F | 2.315 | 1.00 |
| 87_I | 91_A | 2.204 | 1.00 |
| 64_P | 67_V | 2.153 | 1.00 |
| 144_V | 149_L | 2.150 | 1.00 |
| 54_R | 65_N | 2.139 | 1.00 |
| 56_A | 169_F | 2.115 | 1.00 |
| 48_I | 158_L | 2.093 | 1.00 |
| 81_S | 84_I | 2.053 | 1.00 |
| 114_R | 146_M | 2.007 | 1.00 |
| 127_A | 131_R | 1.994 | 1.00 |
| 68_L | 72_A | 1.986 | 1.00 |
| 46_I | 79_I | 1.982 | 1.00 |
| 93_Q | 97_E | 1.981 | 1.00 |
| 122_R | 125_D | 1.981 | 1.00 |
| 49_V | 218_L | 1.867 | 1.00 |
| 42_S | 79_I | 1.768 | 1.00 |
| 25_V | 29_S | 1.732 | 1.00 |
| 129_F | 155_T | 1.727 | 1.00 |
| 92_Y | 96_S | 1.715 | 1.00 |
| 118_L | 141_P | 1.674 | 1.00 |
| 83_V | 86_K | 1.668 | 1.00 |
| 32_F | 36_I | 1.660 | 1.00 |
| 50_F | 214_L | 1.650 | 1.00 |
| 46_I | 222_F | 1.649 | 1.00 |
| 135_S | 145_P | 1.647 | 1.00 |
| 108_K | 111_Q | 1.628 | 1.00 |
| 118_L | 146_M | 1.616 | 1.00 |
| 146_M | 150_L | 1.583 | 1.00 |
| 90_D | 108_K | 1.560 | 0.99 |
| 124_A | 212_Q | 1.519 | 0.99 |
| 216_G | 220_Q | 1.517 | 0.99 |
| 70_G | 154_V | 1.514 | 0.99 |
| 29_S | 36_I | 1.475 | 0.99 |
| 114_R | 149_L | 1.458 | 0.99 |
| 39_M | 154_V | 1.456 | 0.99 |
| 52_L | 202_L | 1.434 | 0.99 |
| 88_Y | 92_Y | 1.433 | 0.99 |
| 132_L | 219_A | 1.423 | 0.99 |
| 93_Q | 96_S | 1.397 | 0.99 |
| 21_V | 25_V | 1.375 | 0.98 |
| 118_L | 149_L | 1.359 | 0.98 |
| 45_R | 222_F | 1.355 | 0.98 |
| 130_A | 133_A | 1.345 | 0.98 |
| 186_L | 195_T | 1.340 | 0.98 |
| 54_R | 63_P | 1.330 | 0.98 |
| 174_I | 178_V | 1.315 | 0.98 |
| 116_F | 153_Y | 1.288 | 0.97 |
| 104_E | 108_K | 1.281 | 0.97 |
| 109_G | 112_P | 1.271 | 0.97 |
| 86_K | 115_A | 1.255 | 0.97 |
| 110_A | 114_R | 1.247 | 0.97 |
| 170_I | 174_I | 1.242 | 0.96 |
| 52_L | 59_T | 1.221 | 0.96 |
| 61_S | 194_A | 1.216 | 0.96 |
| 40_M | 113_L | 1.214 | 0.96 |
| 104_E | 107_D | 1.183 | 0.95 |
| 159_K | 163_Q | 1.148 | 0.94 |
| 190_M | 197_A | 1.145 | 0.94 |
| 164_I | 218_L | 1.142 | 0.94 |
| 209_D | 212_Q | 1.139 | 0.93 |
| 91_A | 109_G | 1.138 | 0.93 |
| 156_S | 160_T | 1.129 | 0.93 |
| 85_D | 147_R | 1.125 | 0.93 |
| 29_S | 32_F | 1.111 | 0.92 |
| 168_I | 208_V | 1.100 | 0.92 |
| 89_V | 93_Q | 1.098 | 0.92 |
| 169_F | 173_L | 1.095 | 0.92 |
| 19_L | 22_Q | 1.094 | 0.92 |
| 76_T | 84_I | 1.092 | 0.91 |
| 84_I | 92_Y | 1.065 | 0.90 |
| 130_A | 138_L | 1.052 | 0.89 |
| 35_A | 38_L | 1.038 | 0.89 |
| 145_P | 148_I | 1.035 | 0.88 |
| 155_T | 212_Q | 1.026 | 0.88 |
| 155_T | 215_M | 1.023 | 0.88 |
| 88_Y | 91_A | 1.021 | 0.87 |
| 140_G | 143_A | 1.015 | 0.87 |
| 30_L | 152_A | 1.008 | 0.86 |
| 33_L | 192_P | 1.001 | 0.86 |
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 | |
| 1rh5B | 1 | 0.2232 | 6.9 | 0.972 | Contact Map |
| 4w252 | 1 | 0.2768 | 6.1 | 0.972 | Contact Map |
| 2ww9B | 1 | 0.2679 | 3.5 | 0.975 | Contact Map |
| 1co4A | 1 | 0.0893 | 3.4 | 0.976 | Contact Map |
| 3mp7B | 1 | 0.2143 | 2.3 | 0.978 | Contact Map |
| 3jstA | 2 | 0.1384 | 2.1 | 0.978 | Contact Map |
| 1m45B | 1 | 0.1116 | 2.1 | 0.978 | Contact Map |
| 3thiA | 1 | 0.3393 | 1.9 | 0.979 | Contact Map |
| 2f6mA | 2 | 0.2812 | 1.8 | 0.979 | Contact Map |
| 2mk9A | 2 | 0.0848 | 1.4 | 0.98 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)