| etx5 15-148 |
| ID: | 1485930650 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 134 (122) | ||
| Sequences: | 123 (55.6) | ||
| Seq/Len: | 1.008 | ||
| Nf(neff/√len): | 5.0 |
Jackhmmer Results: (2016_04)
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: 1.008).
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 |
| 101_S | 133_I | 1.903 | 0.94 |
| 80_E | 122_I | 1.648 | 0.85 |
| 128_T | 132_V | 1.646 | 0.85 |
| 37_L | 54_P | 1.574 | 0.81 |
| 106_K | 109_E | 1.546 | 0.80 |
| 85_N | 99_Y | 1.515 | 0.78 |
| 76_L | 81_S | 1.500 | 0.77 |
| 17_Q | 21_P | 1.486 | 0.76 |
| 59_E | 99_Y | 1.433 | 0.72 |
| 124_A | 128_T | 1.393 | 0.69 |
| 81_S | 86_N | 1.378 | 0.68 |
| 14_L | 20_S | 1.369 | 0.67 |
| 101_S | 104_K | 1.362 | 0.67 |
| 92_E | 112_R | 1.306 | 0.62 |
| 17_Q | 20_S | 1.299 | 0.61 |
| 106_K | 114_K | 1.295 | 0.61 |
| 33_K | 37_L | 1.287 | 0.60 |
| 119_A | 122_I | 1.279 | 0.59 |
| 91_M | 125_A | 1.275 | 0.59 |
| 117_K | 131_L | 1.272 | 0.59 |
| 99_Y | 116_C | 1.265 | 0.58 |
| 67_D | 89_Y | 1.257 | 0.57 |
| 28_L | 107_E | 1.254 | 0.57 |
| 67_D | 75_D | 1.236 | 0.56 |
| 74_L | 77_Q | 1.224 | 0.54 |
| 96_T | 102_L | 1.207 | 0.53 |
| 36_P | 54_P | 1.204 | 0.53 |
| 55_S | 61_Y | 1.201 | 0.52 |
| 101_S | 117_K | 1.177 | 0.50 |
| 82_L | 88_E | 1.163 | 0.49 |
| 91_M | 121_L | 1.161 | 0.49 |
| 25_P | 36_P | 1.155 | 0.48 |
| 60_E | 126_A | 1.153 | 0.48 |
| 24_Y | 27_S | 1.149 | 0.47 |
| 101_S | 108_A | 1.145 | 0.47 |
| 98_G | 116_C | 1.144 | 0.47 |
| 35_N | 54_P | 1.143 | 0.47 |
| 124_A | 132_V | 1.140 | 0.47 |
| 36_P | 55_S | 1.134 | 0.46 |
| 119_A | 133_I | 1.133 | 0.46 |
| 105_R | 111_R | 1.128 | 0.46 |
| 99_Y | 115_V | 1.127 | 0.45 |
| 89_Y | 114_K | 1.124 | 0.45 |
| 27_S | 38_Y | 1.122 | 0.45 |
| 98_G | 106_K | 1.120 | 0.45 |
| 94_I | 99_Y | 1.119 | 0.45 |
| 106_K | 116_C | 1.115 | 0.44 |
| 85_N | 116_C | 1.113 | 0.44 |
| 13_F | 117_K | 1.109 | 0.44 |
| 104_K | 111_R | 1.101 | 0.43 |
| 35_N | 48_E | 1.091 | 0.42 |
| 35_N | 55_S | 1.084 | 0.42 |
| 92_E | 117_K | 1.076 | 0.41 |
| 45_E | 59_E | 1.072 | 0.40 |
| 8_Q | 45_E | 1.065 | 0.40 |
| 92_E | 101_S | 1.052 | 0.39 |
| 113_A | 120_A | 1.049 | 0.38 |
| 23_P | 28_L | 1.031 | 0.37 |
| 126_A | 131_L | 1.029 | 0.37 |
| 38_Y | 48_E | 1.027 | 0.36 |
| 37_L | 60_E | 1.024 | 0.36 |
| 16_E | 23_P | 1.024 | 0.36 |
| 16_E | 19_F | 1.024 | 0.36 |
| 107_E | 127_C | 1.024 | 0.36 |
| 109_E | 117_K | 1.022 | 0.36 |
| 109_E | 127_C | 1.021 | 0.36 |
| 63_R | 83_N | 1.017 | 0.36 |
| 21_P | 27_S | 1.012 | 0.35 |
| 106_K | 110_F | 1.006 | 0.35 |
| 111_R | 120_A | 1.000 | 0.34 |
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 | |
| 3hd7A | 2 | 0.4925 | 7.9 | 0.959 | Contact Map |
| 3fdeA | 2 | 0.6866 | 7.7 | 0.96 | Contact Map |
| 2iw2A | 2 | 0.3284 | 6 | 0.962 | Contact Map |
| 2kogA | 1 | 0.791 | 5.6 | 0.962 | Contact Map |
| 2brqC | 2 | 0.097 | 5.5 | 0.962 | Contact Map |
| 4qinA | 1 | 0.791 | 4.6 | 0.964 | Contact Map |
| 1pi7A | 1 | 0.1119 | 4.1 | 0.965 | Contact Map |
| 4tkrA | 2 | 0.194 | 4.1 | 0.965 | Contact Map |
| 2jp3A | 1 | 0.2612 | 3.7 | 0.965 | Contact Map |
| 3fymA | 1 | 0.4179 | 3 | 0.967 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)