| T0814 240-360 |
| ID: | 1404852198 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 121 (120) | ||
| Sequences: | 223 (205.7) | ||
| Seq/Len: | 1.858 | ||
| Nf(neff/√len): | 18.8 |
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: 1.858).
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 | 6.489 | 1.00 |
| 106_M | 117_K | 2.504 | 1.00 |
| 88_S | 105_K | 2.414 | 1.00 |
| 5_E | 53_D | 2.000 | 0.99 |
| 32_N | 76_H | 1.931 | 0.98 |
| 90_Y | 104_S | 1.902 | 0.98 |
| 37_T | 78_T | 1.878 | 0.98 |
| 58_I | 87_G | 1.816 | 0.97 |
| 14_N | 73_Y | 1.762 | 0.97 |
| 5_E | 51_D | 1.734 | 0.96 |
| 21_V | 35_L | 1.666 | 0.95 |
| 101_D | 104_S | 1.651 | 0.95 |
| 96_F | 104_S | 1.566 | 0.92 |
| 90_Y | 105_K | 1.524 | 0.91 |
| 7_R | 38_D | 1.415 | 0.86 |
| 60_C | 63_C | 1.413 | 0.86 |
| 2_A | 111_E | 1.342 | 0.82 |
| 11_F | 73_Y | 1.310 | 0.80 |
| 53_D | 97_N | 1.297 | 0.79 |
| 104_S | 119_V | 1.277 | 0.77 |
| 6_Y | 98_N | 1.274 | 0.77 |
| 95_L | 104_S | 1.261 | 0.76 |
| 6_Y | 31_Y | 1.258 | 0.76 |
| 58_I | 75_V | 1.256 | 0.76 |
| 55_R | 94_E | 1.252 | 0.75 |
| 13_S | 71_D | 1.243 | 0.74 |
| 6_Y | 105_K | 1.238 | 0.74 |
| 91_L | 119_V | 1.237 | 0.74 |
| 6_Y | 59_R | 1.210 | 0.72 |
| 112_T | 116_E | 1.209 | 0.72 |
| 44_G | 78_T | 1.206 | 0.71 |
| 10_E | 49_D | 1.202 | 0.71 |
| 83_P | 110_F | 1.181 | 0.69 |
| 18_G | 64_N | 1.179 | 0.69 |
| 33_V | 73_Y | 1.172 | 0.68 |
| 12_L | 52_Q | 1.148 | 0.66 |
| 108_Y | 114_Q | 1.142 | 0.65 |
| 17_N | 21_V | 1.142 | 0.65 |
| 81_C | 84_L | 1.141 | 0.65 |
| 74_I | 118_A | 1.137 | 0.65 |
| 63_C | 70_A | 1.137 | 0.65 |
| 83_P | 91_L | 1.128 | 0.64 |
| 75_V | 110_F | 1.096 | 0.60 |
| 2_A | 120_L | 1.077 | 0.58 |
| 6_Y | 49_D | 1.060 | 0.57 |
| 88_S | 119_V | 1.058 | 0.56 |
| 37_T | 114_Q | 1.047 | 0.55 |
| 5_E | 79_L | 1.020 | 0.52 |
| 49_D | 52_Q | 1.017 | 0.52 |
| 106_M | 119_V | 1.009 | 0.51 |
| 12_L | 95_L | 1.007 | 0.51 |
| 38_D | 106_M | 1.004 | 0.51 |
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 | |
| 4aefA | 2 | 0.4876 | 90.5 | 0.881 | Contact Map |
| 2qlvB | 2 | 0.3884 | 86.5 | 0.889 | Contact Map |
| 2z0bA | 6 | 0.4711 | 85.3 | 0.891 | Contact Map |
| 4aeeA | 2 | 0.4959 | 85.3 | 0.891 | Contact Map |
| 1ac0A | 1 | 0.4545 | 82 | 0.895 | Contact Map |
| 2lu3A | 1 | 0.4876 | 68.8 | 0.906 | Contact Map |
| 1z0nA | 3 | 0.3471 | 58.5 | 0.912 | Contact Map |
| 1ea9C | 2 | 0.5702 | 38.9 | 0.922 | Contact Map |
| 1vemA | 1 | 0.9174 | 37.3 | 0.923 | Contact Map |
| 1m7xA | 4 | 0.5372 | 33.7 | 0.924 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)