| T0782 |
| ID: | 1400260158 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 135 (131) | ||
| Sequences: | 334 (266.5) | ||
| Seq/Len: | 2.550 | ||
| Nf(neff/√len): | 23.3 |
HHblits Results: (2013_03)
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: 2.550).
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 |
| 69_G | 132_F | 2.272 | 1.00 |
| 13_L | 119_S | 2.118 | 1.00 |
| 28_L | 116_L | 2.002 | 0.99 |
| 54_F | 124_E | 1.504 | 0.94 |
| 2_M | 92_S | 1.491 | 0.94 |
| 54_F | 89_L | 1.485 | 0.94 |
| 38_Q | 107_G | 1.457 | 0.93 |
| 14_V | 20_A | 1.451 | 0.93 |
| 18_L | 36_Q | 1.430 | 0.92 |
| 77_Y | 107_G | 1.419 | 0.92 |
| 94_N | 97_N | 1.405 | 0.91 |
| 46_K | 108_K | 1.397 | 0.91 |
| 20_A | 112_K | 1.395 | 0.91 |
| 35_R | 133_R | 1.391 | 0.91 |
| 30_G | 55_Q | 1.360 | 0.89 |
| 38_Q | 128_T | 1.358 | 0.89 |
| 84_I | 101_Y | 1.323 | 0.87 |
| 73_F | 89_L | 1.308 | 0.87 |
| 79_L | 91_E | 1.281 | 0.85 |
| 82_A | 108_K | 1.250 | 0.83 |
| 66_K | 69_G | 1.242 | 0.82 |
| 17_T | 54_F | 1.226 | 0.81 |
| 9_L | 12_V | 1.223 | 0.81 |
| 77_Y | 110_T | 1.200 | 0.79 |
| 3_K | 7_K | 1.187 | 0.78 |
| 50_V | 76_N | 1.184 | 0.78 |
| 14_V | 18_L | 1.180 | 0.78 |
| 33_Q | 76_N | 1.176 | 0.77 |
| 25_G | 52_Y | 1.176 | 0.77 |
| 80_K | 83_E | 1.175 | 0.77 |
| 26_G | 44_S | 1.172 | 0.77 |
| 54_F | 78_S | 1.153 | 0.75 |
| 29_A | 79_L | 1.146 | 0.75 |
| 77_Y | 90_P | 1.137 | 0.74 |
| 96_K | 100_T | 1.133 | 0.74 |
| 14_V | 43_T | 1.128 | 0.73 |
| 11_I | 17_T | 1.120 | 0.72 |
| 113_V | 116_L | 1.116 | 0.72 |
| 95_D | 98_Y | 1.115 | 0.72 |
| 80_K | 112_K | 1.106 | 0.71 |
| 31_K | 130_S | 1.104 | 0.71 |
| 52_Y | 75_G | 1.098 | 0.70 |
| 31_K | 53_N | 1.089 | 0.69 |
| 12_V | 15_A | 1.087 | 0.69 |
| 83_E | 132_F | 1.086 | 0.69 |
| 92_S | 96_K | 1.084 | 0.69 |
| 14_V | 120_S | 1.083 | 0.69 |
| 11_I | 44_S | 1.080 | 0.68 |
| 2_M | 7_K | 1.073 | 0.68 |
| 88_L | 132_F | 1.065 | 0.67 |
| 13_L | 121_L | 1.061 | 0.66 |
| 63_C | 71_T | 1.061 | 0.66 |
| 36_Q | 131_I | 1.059 | 0.66 |
| 88_L | 104_W | 1.057 | 0.66 |
| 54_F | 131_I | 1.056 | 0.66 |
| 87_I | 126_E | 1.056 | 0.66 |
| 119_S | 134_K | 1.056 | 0.66 |
| 67_D | 77_Y | 1.052 | 0.65 |
| 112_K | 124_E | 1.049 | 0.65 |
| 31_K | 51_F | 1.048 | 0.65 |
| 38_Q | 61_A | 1.046 | 0.65 |
| 46_K | 117_S | 1.036 | 0.64 |
| 104_W | 130_S | 1.032 | 0.63 |
| 54_F | 108_K | 1.029 | 0.63 |
| 65_L | 122_R | 1.026 | 0.63 |
| 37_Y | 122_R | 1.023 | 0.62 |
| 30_G | 56_K | 1.022 | 0.62 |
| 72_T | 122_R | 1.021 | 0.62 |
| 114_E | 123_L | 1.014 | 0.61 |
| 83_E | 129_K | 1.010 | 0.61 |
| 18_L | 112_K | 1.004 | 0.60 |
| 20_A | 23_N | 1.004 | 0.60 |
| 18_L | 37_Y | 1.001 | 0.60 |
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 | |
| 2ktsA | 1 | 0.763 | 98.6 | 0.63 | Contact Map |
| 2la7A | 1 | 0.9111 | 98.3 | 0.671 | Contact Map |
| 3htyA | 16 | 0.6889 | 93.7 | 0.8 | Contact Map |
| 2m4lA | 1 | 0.7185 | 79.3 | 0.844 | Contact Map |
| 3zbiC | 14 | 0.2 | 78.7 | 0.845 | Contact Map |
| 3p24A | 4 | 0.5926 | 61.7 | 0.863 | Contact Map |
| 3ucpA | 1 | 0.4963 | 56.8 | 0.867 | Contact Map |
| 4lmhA | 4 | 0.5259 | 41.7 | 0.878 | Contact Map |
| 3pmqA | 1 | 0.5556 | 35.7 | 0.883 | Contact Map |
| 4iabA | 4 | 0.837 | 34.7 | 0.884 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)