| Ts814_d03 |
| ID: | 1406133569 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 151 (147) | ||
| Sequences: | 517 (444.4) | ||
| Seq/Len: | 3.517 | ||
| Nf(neff/√len): | 36.7 |
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: 3.517).
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 | 4.668 | 1.00 |
| 106_M | 117_K | 2.988 | 1.00 |
| 38_D | 130_Y | 2.246 | 1.00 |
| 139_V | 142_T | 1.947 | 1.00 |
| 88_S | 105_K | 1.880 | 1.00 |
| 137_S | 140_G | 1.773 | 0.99 |
| 46_Y | 51_D | 1.646 | 0.98 |
| 90_Y | 104_S | 1.552 | 0.98 |
| 136_G | 140_G | 1.532 | 0.97 |
| 128_Y | 140_G | 1.501 | 0.97 |
| 137_S | 142_T | 1.493 | 0.97 |
| 137_S | 141_Q | 1.492 | 0.97 |
| 77_F | 119_V | 1.417 | 0.95 |
| 7_R | 13_S | 1.411 | 0.95 |
| 46_Y | 54_G | 1.410 | 0.95 |
| 136_G | 139_V | 1.387 | 0.94 |
| 11_F | 73_Y | 1.371 | 0.94 |
| 60_C | 63_C | 1.365 | 0.94 |
| 134_P | 138_S | 1.361 | 0.94 |
| 96_F | 119_V | 1.345 | 0.93 |
| 13_S | 16_Y | 1.343 | 0.93 |
| 141_Q | 144_P | 1.328 | 0.93 |
| 133_V | 136_G | 1.327 | 0.93 |
| 90_Y | 105_K | 1.302 | 0.92 |
| 95_L | 126_Y | 1.284 | 0.91 |
| 55_R | 60_C | 1.272 | 0.90 |
| 17_N | 21_V | 1.230 | 0.88 |
| 140_G | 144_P | 1.225 | 0.88 |
| 91_L | 119_V | 1.221 | 0.88 |
| 14_N | 73_Y | 1.214 | 0.87 |
| 140_G | 145_I | 1.206 | 0.87 |
| 77_F | 128_Y | 1.204 | 0.87 |
| 74_I | 118_A | 1.204 | 0.87 |
| 137_S | 144_P | 1.201 | 0.87 |
| 72_Y | 122_K | 1.198 | 0.86 |
| 13_S | 18_G | 1.188 | 0.86 |
| 6_Y | 98_N | 1.181 | 0.85 |
| 74_I | 120_L | 1.172 | 0.85 |
| 7_R | 12_L | 1.166 | 0.84 |
| 7_R | 11_F | 1.156 | 0.84 |
| 58_I | 61_S | 1.155 | 0.84 |
| 128_Y | 139_V | 1.135 | 0.82 |
| 97_N | 130_Y | 1.127 | 0.81 |
| 5_E | 51_D | 1.122 | 0.81 |
| 94_E | 98_N | 1.122 | 0.81 |
| 51_D | 54_G | 1.121 | 0.81 |
| 142_T | 145_I | 1.121 | 0.81 |
| 5_E | 53_D | 1.117 | 0.81 |
| 127_N | 136_G | 1.113 | 0.80 |
| 136_G | 141_Q | 1.106 | 0.80 |
| 139_V | 145_I | 1.105 | 0.80 |
| 21_V | 25_S | 1.101 | 0.79 |
| 49_D | 52_Q | 1.095 | 0.79 |
| 115_Y | 132_F | 1.092 | 0.79 |
| 37_T | 78_T | 1.090 | 0.78 |
| 143_G | 147_G | 1.069 | 0.76 |
| 32_N | 35_L | 1.066 | 0.76 |
| 77_F | 137_S | 1.065 | 0.76 |
| 8_R | 13_S | 1.057 | 0.75 |
| 6_Y | 105_K | 1.047 | 0.74 |
| 46_Y | 49_D | 1.043 | 0.74 |
| 46_Y | 56_F | 1.043 | 0.74 |
| 80_A | 107_G | 1.042 | 0.74 |
| 54_G | 71_D | 1.040 | 0.74 |
| 8_R | 98_N | 1.039 | 0.74 |
| 83_P | 86_D | 1.038 | 0.73 |
| 139_V | 144_P | 1.028 | 0.72 |
| 56_F | 59_R | 1.027 | 0.72 |
| 108_Y | 115_Y | 1.026 | 0.72 |
| 79_L | 106_M | 1.024 | 0.72 |
| 11_F | 14_N | 1.023 | 0.72 |
| 71_D | 109_N | 1.022 | 0.72 |
| 129_Q | 136_G | 1.019 | 0.71 |
| 122_K | 126_Y | 1.018 | 0.71 |
| 66_P | 91_L | 1.015 | 0.71 |
| 81_C | 86_D | 1.010 | 0.70 |
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 | 99.7 | 0.498 | Contact Map |
| 4aefA | 2 | 0.5894 | 99.6 | 0.545 | Contact Map |
| 4aeeA | 2 | 0.6026 | 99.5 | 0.551 | Contact Map |
| 4cfeB | 2 | 0.4636 | 99.5 | 0.559 | Contact Map |
| 4pyhA | 1 | 0.8543 | 99.5 | 0.573 | Contact Map |
| 2lu3A | 1 | 0.5894 | 99.4 | 0.583 | Contact Map |
| 1z0nA | 3 | 0.4768 | 99.4 | 0.584 | Contact Map |
| 1ac0A | 1 | 0.5563 | 98.8 | 0.677 | Contact Map |
| 2z0bA | 6 | 0.5762 | 98.6 | 0.701 | Contact Map |
| 1m7xA | 4 | 0.6225 | 98.3 | 0.724 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)