| YfiR |
| ID: | 1423055954 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 155 (147) | ||
| Sequences: | 285 (241.8) | ||
| Seq/Len: | 1.939 | ||
| Nf(neff/√len): | 19.9 |
HHblits Results: (2013_03)
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: 1.939).
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 |
| 20_I | 116_F | 3.790 | 1.00 |
| 36_C | 75_C | 3.768 | 1.00 |
| 109_E | 114_S | 3.759 | 1.00 |
| 101_L | 139_V | 2.466 | 1.00 |
| 104_S | 114_S | 2.186 | 1.00 |
| 104_S | 109_E | 1.982 | 0.99 |
| 36_C | 117_C | 1.969 | 0.99 |
| 115_M | 134_I | 1.967 | 0.99 |
| 134_I | 141_V | 1.860 | 0.98 |
| 15_Q | 19_G | 1.687 | 0.96 |
| 127_F | 148_L | 1.661 | 0.95 |
| 117_C | 128_E | 1.606 | 0.94 |
| 19_G | 22_S | 1.581 | 0.93 |
| 34_Q | 76_N | 1.543 | 0.92 |
| 27_P | 99_P | 1.498 | 0.91 |
| 77_V | 103_I | 1.494 | 0.90 |
| 23_Y | 48_L | 1.490 | 0.90 |
| 128_E | 150_R | 1.448 | 0.88 |
| 116_F | 143_P | 1.442 | 0.88 |
| 8_Q | 11_N | 1.430 | 0.88 |
| 109_E | 113_G | 1.389 | 0.86 |
| 17_L | 103_I | 1.370 | 0.84 |
| 21_F | 79_Y | 1.360 | 0.84 |
| 33_L | 118_L | 1.355 | 0.84 |
| 35_L | 127_F | 1.355 | 0.84 |
| 102_S | 105_E | 1.353 | 0.83 |
| 77_V | 101_L | 1.349 | 0.83 |
| 23_Y | 145_V | 1.330 | 0.82 |
| 42_E | 79_Y | 1.291 | 0.79 |
| 127_F | 151_R | 1.285 | 0.79 |
| 100_V | 149_A | 1.250 | 0.76 |
| 36_C | 64_R | 1.219 | 0.74 |
| 91_V | 129_A | 1.208 | 0.73 |
| 32_V | 76_N | 1.186 | 0.71 |
| 48_L | 63_R | 1.183 | 0.70 |
| 146_L | 149_A | 1.183 | 0.70 |
| 44_A | 48_L | 1.180 | 0.70 |
| 76_N | 83_V | 1.170 | 0.69 |
| 104_S | 110_C | 1.159 | 0.68 |
| 23_Y | 114_S | 1.156 | 0.68 |
| 21_F | 24_V | 1.154 | 0.68 |
| 79_Y | 135_A | 1.152 | 0.67 |
| 110_C | 130_N | 1.144 | 0.67 |
| 116_F | 132_D | 1.136 | 0.66 |
| 8_Q | 12_A | 1.126 | 0.65 |
| 115_M | 137_S | 1.124 | 0.65 |
| 16_V | 79_Y | 1.112 | 0.63 |
| 134_I | 145_V | 1.105 | 0.63 |
| 78_I | 149_A | 1.099 | 0.62 |
| 28_K | 94_S | 1.095 | 0.62 |
| 88_R | 117_C | 1.088 | 0.61 |
| 39_G | 134_I | 1.084 | 0.61 |
| 41_T | 105_E | 1.075 | 0.60 |
| 25_R | 117_C | 1.072 | 0.59 |
| 23_Y | 59_V | 1.069 | 0.59 |
| 24_V | 139_V | 1.064 | 0.58 |
| 16_V | 103_I | 1.064 | 0.58 |
| 72_G | 100_V | 1.056 | 0.58 |
| 144_S | 147_K | 1.052 | 0.57 |
| 39_G | 102_S | 1.045 | 0.56 |
| 20_I | 144_S | 1.040 | 0.56 |
| 91_V | 130_N | 1.024 | 0.54 |
| 36_C | 118_L | 1.023 | 0.54 |
| 112_V | 124_R | 1.022 | 0.54 |
| 7_E | 11_N | 1.013 | 0.53 |
| 102_S | 134_I | 1.013 | 0.53 |
| 43_Y | 125_I | 1.007 | 0.52 |
| 38_V | 83_V | 1.003 | 0.52 |
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 | |
| 1wwkA | 2 | 0.9806 | 32.3 | 0.929 | Contact Map |
| 4s1vD | 4 | 0.9742 | 26.2 | 0.932 | Contact Map |
| 2r00A | 2 | 0.6774 | 23.7 | 0.933 | Contact Map |
| 2cukA | 4 | 0.9742 | 22.7 | 0.934 | Contact Map |
| 1gdhA | 2 | 0.9613 | 18.7 | 0.936 | Contact Map |
| 2gcgA | 4 | 0.9806 | 18.4 | 0.937 | Contact Map |
| 4g2nA | 4 | 0.9742 | 14.3 | 0.94 | Contact Map |
| 3gg9A | 4 | 0.9742 | 14.2 | 0.94 | Contact Map |
| 4hy3A | 4 | 0.9677 | 12.8 | 0.941 | Contact Map |
| 2dbqA | 1 | 0.9677 | 12.6 | 0.941 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)