| T0774 - TR774 |
| ID: | 1402955375 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 157 (150) | ||
| Sequences: | 217 (189.7) | ||
| Seq/Len: | 1.447 | ||
| Nf(neff/√len): | 15.5 |
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: 1.447).
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 |
| 89_A | 133_V | 2.743 | 1.00 |
| 77_P | 83_I | 2.640 | 1.00 |
| 36_A | 56_M | 2.343 | 0.99 |
| 33_G | 91_Y | 2.291 | 0.99 |
| 33_G | 88_Y | 2.224 | 0.99 |
| 70_Y | 74_R | 2.072 | 0.98 |
| 33_G | 58_N | 1.901 | 0.97 |
| 125_N | 128_D | 1.744 | 0.94 |
| 32_F | 156_F | 1.729 | 0.94 |
| 61_A | 68_W | 1.675 | 0.92 |
| 130_I | 133_V | 1.641 | 0.91 |
| 53_P | 112_G | 1.638 | 0.91 |
| 82_K | 86_F | 1.625 | 0.91 |
| 53_P | 57_Y | 1.599 | 0.90 |
| 36_A | 77_P | 1.575 | 0.89 |
| 36_A | 83_I | 1.563 | 0.88 |
| 58_N | 91_Y | 1.545 | 0.88 |
| 70_Y | 154_F | 1.502 | 0.86 |
| 36_A | 55_F | 1.501 | 0.85 |
| 36_A | 118_F | 1.500 | 0.85 |
| 118_F | 121_K | 1.445 | 0.82 |
| 152_V | 156_F | 1.445 | 0.82 |
| 34_I | 74_R | 1.443 | 0.82 |
| 135_D | 156_F | 1.404 | 0.80 |
| 37_Y | 82_K | 1.364 | 0.77 |
| 61_A | 70_Y | 1.362 | 0.77 |
| 56_M | 83_I | 1.361 | 0.77 |
| 120_V | 129_M | 1.331 | 0.75 |
| 26_L | 30_A | 1.325 | 0.74 |
| 18_G | 89_A | 1.306 | 0.73 |
| 121_K | 125_N | 1.290 | 0.71 |
| 86_F | 114_P | 1.290 | 0.71 |
| 86_F | 134_T | 1.289 | 0.71 |
| 78_I | 142_D | 1.287 | 0.71 |
| 68_W | 118_F | 1.261 | 0.69 |
| 129_M | 142_D | 1.253 | 0.68 |
| 77_P | 89_A | 1.240 | 0.67 |
| 55_F | 83_I | 1.239 | 0.67 |
| 55_F | 77_P | 1.217 | 0.65 |
| 68_W | 75_F | 1.215 | 0.65 |
| 54_N | 58_N | 1.206 | 0.64 |
| 61_A | 76_W | 1.202 | 0.63 |
| 61_A | 154_F | 1.185 | 0.62 |
| 24_S | 63_W | 1.175 | 0.61 |
| 70_Y | 84_T | 1.173 | 0.61 |
| 91_Y | 104_T | 1.168 | 0.60 |
| 36_A | 61_A | 1.162 | 0.60 |
| 20_E | 118_F | 1.148 | 0.58 |
| 7_G | 18_G | 1.131 | 0.56 |
| 27_K | 31_G | 1.124 | 0.56 |
| 22_T | 136_C | 1.122 | 0.56 |
| 3_N | 7_G | 1.121 | 0.55 |
| 142_D | 150_G | 1.119 | 0.55 |
| 103_I | 154_F | 1.119 | 0.55 |
| 68_W | 133_V | 1.111 | 0.54 |
| 59_E | 72_N | 1.107 | 0.54 |
| 37_Y | 77_P | 1.092 | 0.52 |
| 66_D | 152_V | 1.088 | 0.52 |
| 36_A | 122_T | 1.079 | 0.51 |
| 82_K | 141_Q | 1.065 | 0.50 |
| 23_T | 26_L | 1.064 | 0.50 |
| 68_W | 132_L | 1.051 | 0.48 |
| 148_N | 151_T | 1.038 | 0.47 |
| 32_F | 118_F | 1.037 | 0.47 |
| 35_F | 80_D | 1.032 | 0.46 |
| 57_Y | 112_G | 1.027 | 0.46 |
| 42_A | 46_S | 1.025 | 0.46 |
| 56_M | 61_A | 1.004 | 0.43 |
| 68_W | 76_W | 1.003 | 0.43 |
| 31_G | 60_H | 1.002 | 0.43 |
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 | |
| 4epsA | 1 | 0.828 | 99.7 | 0.538 | Contact Map |
| 3sy6A | 2 | 0.8089 | 99.6 | 0.573 | Contact Map |
| 4k4kA | 2 | 0.7516 | 99.6 | 0.58 | Contact Map |
| 3ufiA | 1 | 0.8153 | 99.5 | 0.609 | Contact Map |
| 3t2lA | 1 | 0.7771 | 99.4 | 0.615 | Contact Map |
| 4dguA | 2 | 0.6688 | 98 | 0.766 | Contact Map |
| 3irpX | 1 | 0.6306 | 4.8 | 0.941 | Contact Map |
| 2ebnA | 1 | 0.3822 | 1.3 | 0.956 | Contact Map |
| 1ux6A | 1 | 0.3376 | 1.1 | 0.958 | Contact Map |
| 1bmlC | 2 | 0.3439 | 0.9 | 0.961 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)