| Q9HYR3_1Z1S |
| ID: | 1404256883 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (133) | ||
| Sequences: | 323 (270) | ||
| Seq/Len: | 2.429 | ||
| Nf(neff/√len): | 23.4 |
Jackhmmer Results: (2014_04_16)
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: 2.429).
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 |
| 83_E | 116_R | 2.290 | 1.00 |
| 30_G | 51_I | 2.284 | 1.00 |
| 26_F | 30_G | 2.155 | 1.00 |
| 6_I | 107_T | 1.886 | 0.99 |
| 108_R | 113_L | 1.882 | 0.99 |
| 31_V | 44_R | 1.828 | 0.99 |
| 87_D | 98_A | 1.825 | 0.99 |
| 28_P | 111_Q | 1.774 | 0.98 |
| 68_D | 85_H | 1.719 | 0.98 |
| 36_Y | 99_Q | 1.696 | 0.97 |
| 46_E | 50_T | 1.653 | 0.97 |
| 7_L | 80_A | 1.637 | 0.97 |
| 74_T | 77_P | 1.622 | 0.96 |
| 18_D | 21_G | 1.603 | 0.96 |
| 33_E | 44_R | 1.572 | 0.95 |
| 48_R | 56_R | 1.553 | 0.95 |
| 104_V | 117_D | 1.541 | 0.95 |
| 20_R | 52_W | 1.536 | 0.95 |
| 31_V | 114_L | 1.509 | 0.94 |
| 7_L | 82_G | 1.504 | 0.94 |
| 106_R | 114_L | 1.500 | 0.94 |
| 34_F | 119_W | 1.486 | 0.93 |
| 27_H | 113_L | 1.441 | 0.92 |
| 7_L | 105_L | 1.428 | 0.91 |
| 78_D | 108_R | 1.412 | 0.91 |
| 88_G | 97_L | 1.385 | 0.89 |
| 132_E | 135_A | 1.384 | 0.89 |
| 27_H | 36_Y | 1.338 | 0.87 |
| 72_Y | 104_V | 1.336 | 0.87 |
| 63_T | 89_V | 1.329 | 0.87 |
| 26_F | 115_Y | 1.328 | 0.87 |
| 79_L | 106_R | 1.274 | 0.83 |
| 84_F | 103_S | 1.266 | 0.83 |
| 30_G | 114_L | 1.266 | 0.83 |
| 33_E | 114_L | 1.257 | 0.82 |
| 81_I | 104_V | 1.239 | 0.81 |
| 53_A | 75_A | 1.236 | 0.81 |
| 34_F | 115_Y | 1.236 | 0.81 |
| 101_Y | 119_W | 1.234 | 0.81 |
| 84_F | 115_Y | 1.202 | 0.78 |
| 28_P | 49_E | 1.197 | 0.78 |
| 76_D | 106_R | 1.197 | 0.78 |
| 37_A | 119_W | 1.167 | 0.75 |
| 28_P | 113_L | 1.166 | 0.75 |
| 131_V | 134_A | 1.164 | 0.75 |
| 49_E | 52_W | 1.160 | 0.75 |
| 85_H | 100_D | 1.155 | 0.74 |
| 29_E | 47_G | 1.135 | 0.72 |
| 10_S | 22_W | 1.132 | 0.72 |
| 5_E | 98_A | 1.122 | 0.71 |
| 133_A | 136_K | 1.119 | 0.71 |
| 50_T | 53_A | 1.108 | 0.70 |
| 53_A | 56_R | 1.099 | 0.69 |
| 84_F | 101_Y | 1.093 | 0.68 |
| 28_P | 46_E | 1.093 | 0.68 |
| 84_F | 102_I | 1.080 | 0.67 |
| 4_K | 73_E | 1.048 | 0.64 |
| 27_H | 32_L | 1.045 | 0.63 |
| 22_W | 100_D | 1.044 | 0.63 |
| 48_R | 74_T | 1.032 | 0.62 |
| 54_H | 84_F | 1.029 | 0.61 |
| 74_T | 79_L | 1.027 | 0.61 |
| 6_I | 108_R | 1.026 | 0.61 |
| 55_M | 64_V | 1.025 | 0.61 |
| 31_V | 47_G | 1.022 | 0.61 |
| 9_H | 12_R | 1.019 | 0.60 |
| 132_E | 136_K | 1.018 | 0.60 |
| 88_G | 128_L | 1.014 | 0.60 |
| 4_K | 8_V | 1.002 | 0.58 |
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 | |
| 1z1sA | 1 | 0.9149 | 99.9 | 0.492 | Contact Map |
| 1s5aA | 4 | 0.9574 | 99.9 | 0.528 | Contact Map |
| 3jumA | 2 | 0.9858 | 99.9 | 0.56 | Contact Map |
| 3ff0A | 2 | 0.9858 | 99.9 | 0.566 | Contact Map |
| 3grdA | 2 | 0.9007 | 99.8 | 0.577 | Contact Map |
| 3dm8A | 1 | 0.9078 | 99.8 | 0.59 | Contact Map |
| 3fgyA | 2 | 0.922 | 99.8 | 0.595 | Contact Map |
| 2a15A | 1 | 0.9007 | 99.8 | 0.599 | Contact Map |
| 3dmcA | 2 | 0.844 | 99.8 | 0.599 | Contact Map |
| 3i0yA | 4 | 0.8865 | 99.8 | 0.612 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)