| Ts814_d03 |
| ID: | 1406135040 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (150) | ||
| Sequences: | 161 (147.8) | ||
| Seq/Len: | 1.073 | ||
| Nf(neff/√len): | 12.1 |
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: 1.073).
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 |
| 109_N | 116_E | 4.612 | 1.00 |
| 38_D | 130_Y | 2.652 | 1.00 |
| 106_M | 117_K | 2.355 | 0.99 |
| 90_Y | 104_S | 1.816 | 0.92 |
| 14_N | 73_Y | 1.653 | 0.87 |
| 37_T | 78_T | 1.556 | 0.82 |
| 12_L | 125_S | 1.544 | 0.81 |
| 76_H | 126_Y | 1.522 | 0.80 |
| 5_E | 51_D | 1.516 | 0.80 |
| 72_Y | 122_K | 1.508 | 0.79 |
| 2_A | 150_Y | 1.506 | 0.79 |
| 6_Y | 31_Y | 1.498 | 0.78 |
| 109_N | 118_A | 1.454 | 0.75 |
| 134_P | 138_S | 1.449 | 0.75 |
| 9_M | 108_Y | 1.420 | 0.73 |
| 91_L | 138_S | 1.409 | 0.72 |
| 72_Y | 123_Q | 1.392 | 0.71 |
| 46_Y | 122_K | 1.354 | 0.68 |
| 46_Y | 54_G | 1.341 | 0.67 |
| 13_S | 71_D | 1.338 | 0.67 |
| 88_S | 105_K | 1.334 | 0.66 |
| 33_V | 73_Y | 1.323 | 0.65 |
| 70_A | 127_N | 1.323 | 0.65 |
| 6_Y | 59_R | 1.316 | 0.65 |
| 121_L | 126_Y | 1.301 | 0.63 |
| 104_S | 119_V | 1.297 | 0.63 |
| 8_R | 125_S | 1.287 | 0.62 |
| 6_Y | 24_I | 1.285 | 0.62 |
| 51_D | 72_Y | 1.275 | 0.61 |
| 106_M | 119_V | 1.274 | 0.61 |
| 60_C | 63_C | 1.252 | 0.59 |
| 91_L | 119_V | 1.208 | 0.55 |
| 10_E | 151_Q | 1.208 | 0.55 |
| 9_M | 95_L | 1.203 | 0.54 |
| 7_R | 13_S | 1.200 | 0.54 |
| 90_Y | 103_K | 1.192 | 0.53 |
| 11_F | 73_Y | 1.186 | 0.53 |
| 87_G | 134_P | 1.185 | 0.53 |
| 46_Y | 72_Y | 1.180 | 0.52 |
| 129_Q | 141_Q | 1.179 | 0.52 |
| 5_E | 46_Y | 1.171 | 0.51 |
| 7_R | 38_D | 1.140 | 0.48 |
| 54_G | 122_K | 1.139 | 0.48 |
| 49_D | 52_Q | 1.134 | 0.48 |
| 58_I | 87_G | 1.134 | 0.48 |
| 67_D | 73_Y | 1.130 | 0.47 |
| 52_Q | 127_N | 1.129 | 0.47 |
| 51_D | 122_K | 1.127 | 0.47 |
| 62_D | 115_Y | 1.124 | 0.47 |
| 14_N | 19_M | 1.121 | 0.47 |
| 52_Q | 125_S | 1.120 | 0.47 |
| 5_E | 79_L | 1.109 | 0.46 |
| 71_D | 105_K | 1.102 | 0.45 |
| 46_Y | 56_F | 1.097 | 0.44 |
| 147_G | 150_Y | 1.079 | 0.43 |
| 63_C | 66_P | 1.069 | 0.42 |
| 55_R | 94_E | 1.066 | 0.42 |
| 41_R | 65_D | 1.064 | 0.41 |
| 43_K | 135_T | 1.052 | 0.40 |
| 28_N | 40_R | 1.049 | 0.40 |
| 143_G | 148_N | 1.036 | 0.39 |
| 53_D | 107_G | 1.036 | 0.39 |
| 112_T | 116_E | 1.035 | 0.39 |
| 5_E | 54_G | 1.030 | 0.38 |
| 77_F | 139_V | 1.027 | 0.38 |
| 12_L | 50_Q | 1.019 | 0.37 |
| 90_Y | 105_K | 1.011 | 0.37 |
| 71_D | 121_L | 1.010 | 0.36 |
| 26_F | 104_S | 1.009 | 0.36 |
| 16_Y | 21_V | 1.009 | 0.36 |
| 20_H | 96_F | 1.005 | 0.36 |
| 10_E | 51_D | 1.004 | 0.36 |
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 | |
| 2qlvB | 2 | 0.5099 | 98.8 | 0.768 | Contact Map |
| 4aefA | 2 | 0.5894 | 98.7 | 0.775 | Contact Map |
| 4aeeA | 2 | 0.6026 | 98.6 | 0.785 | Contact Map |
| 2lu3A | 1 | 0.5894 | 98.3 | 0.804 | Contact Map |
| 4cfeB | 2 | 0.4636 | 98.3 | 0.804 | Contact Map |
| 4pyhA | 1 | 0.8543 | 98.2 | 0.807 | Contact Map |
| 1z0nA | 3 | 0.4768 | 98.2 | 0.809 | Contact Map |
| 1ac0A | 1 | 0.5563 | 98 | 0.819 | Contact Map |
| 2z0bA | 6 | 0.5695 | 97.8 | 0.827 | Contact Map |
| 1gcyA | 1 | 0.3444 | 97.4 | 0.841 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)