| T0842 |
| ID: | 1404416553 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (139) | ||
| Sequences: | 341 (281.8) | ||
| Seq/Len: | 2.453 | ||
| Nf(neff/√len): | 23.9 |
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: 2.453).
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 |
| 95_K | 103_E | 2.377 | 1.00 |
| 48_V | 87_A | 2.167 | 1.00 |
| 134_E | 137_R | 1.991 | 0.99 |
| 41_V | 44_W | 1.778 | 0.98 |
| 99_R | 102_A | 1.694 | 0.97 |
| 32_P | 41_V | 1.633 | 0.97 |
| 24_I | 124_Q | 1.587 | 0.96 |
| 44_W | 105_G | 1.550 | 0.95 |
| 88_G | 102_A | 1.488 | 0.93 |
| 36_A | 40_E | 1.411 | 0.91 |
| 45_C | 55_L | 1.385 | 0.90 |
| 120_V | 127_I | 1.381 | 0.89 |
| 73_S | 117_T | 1.375 | 0.89 |
| 28_M | 34_V | 1.361 | 0.89 |
| 65_K | 82_S | 1.324 | 0.87 |
| 54_V | 81_T | 1.310 | 0.86 |
| 40_E | 92_C | 1.306 | 0.86 |
| 15_T | 39_Q | 1.299 | 0.85 |
| 121_T | 124_Q | 1.278 | 0.84 |
| 59_M | 112_A | 1.263 | 0.83 |
| 116_Y | 120_V | 1.263 | 0.83 |
| 15_T | 113_L | 1.226 | 0.80 |
| 79_N | 92_C | 1.208 | 0.79 |
| 66_P | 103_E | 1.207 | 0.79 |
| 127_I | 130_V | 1.205 | 0.79 |
| 39_Q | 126_N | 1.201 | 0.78 |
| 61_E | 64_Q | 1.195 | 0.78 |
| 11_A | 142_S | 1.194 | 0.78 |
| 57_E | 82_S | 1.187 | 0.77 |
| 89_R | 100_R | 1.177 | 0.76 |
| 84_H | 119_A | 1.166 | 0.76 |
| 127_I | 131_P | 1.160 | 0.75 |
| 35_Q | 118_S | 1.160 | 0.75 |
| 49_Y | 109_L | 1.155 | 0.75 |
| 25_A | 90_N | 1.139 | 0.73 |
| 60_Q | 106_F | 1.134 | 0.73 |
| 23_E | 127_I | 1.130 | 0.72 |
| 23_E | 27_R | 1.122 | 0.71 |
| 80_P | 102_A | 1.118 | 0.71 |
| 4_H | 7_H | 1.116 | 0.71 |
| 119_A | 122_Q | 1.116 | 0.71 |
| 97_N | 123_A | 1.108 | 0.70 |
| 13_Q | 49_Y | 1.107 | 0.70 |
| 116_Y | 127_I | 1.103 | 0.70 |
| 69_G | 120_V | 1.100 | 0.69 |
| 19_L | 34_V | 1.099 | 0.69 |
| 32_P | 71_D | 1.097 | 0.69 |
| 23_E | 131_P | 1.089 | 0.68 |
| 109_L | 116_Y | 1.088 | 0.68 |
| 131_P | 135_A | 1.088 | 0.68 |
| 20_T | 23_E | 1.083 | 0.68 |
| 128_K | 139_G | 1.075 | 0.67 |
| 88_G | 99_R | 1.072 | 0.66 |
| 34_V | 120_V | 1.069 | 0.66 |
| 28_M | 85_K | 1.067 | 0.66 |
| 48_V | 102_A | 1.061 | 0.65 |
| 111_Q | 117_T | 1.059 | 0.65 |
| 31_N | 139_G | 1.057 | 0.65 |
| 49_Y | 57_E | 1.057 | 0.65 |
| 45_C | 103_E | 1.055 | 0.65 |
| 41_V | 60_Q | 1.053 | 0.64 |
| 57_E | 96_T | 1.051 | 0.64 |
| 8_H | 12_M | 1.051 | 0.64 |
| 66_P | 110_C | 1.048 | 0.64 |
| 70_E | 116_Y | 1.046 | 0.64 |
| 41_V | 93_G | 1.042 | 0.63 |
| 47_I | 87_A | 1.042 | 0.63 |
| 10_V | 142_S | 1.036 | 0.63 |
| 73_S | 133_A | 1.034 | 0.62 |
| 78_E | 100_R | 1.025 | 0.61 |
| 73_S | 114_D | 1.011 | 0.60 |
| 79_N | 96_T | 1.009 | 0.60 |
| 48_V | 94_L | 1.007 | 0.59 |
| 58_K | 82_S | 1.006 | 0.59 |
| 85_K | 103_E | 1.006 | 0.59 |
| 49_Y | 83_V | 1.000 | 0.58 |
| 26_D | 47_I | 1.000 | 0.58 |
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 | |
| 2lnmA | 1 | 0.411 | 39.8 | 0.906 | Contact Map |
| 2llwA | 1 | 0.4863 | 16.3 | 0.922 | Contact Map |
| 3vejA | 2 | 0.274 | 12.5 | 0.926 | Contact Map |
| 2zbcA | 8 | 0.5274 | 9.2 | 0.931 | Contact Map |
| 2ywkA | 1 | 0.5342 | 9 | 0.931 | Contact Map |
| 3hwsA | 6 | 0.6438 | 8.2 | 0.932 | Contact Map |
| 2cqpA | 1 | 0.5685 | 7.8 | 0.933 | Contact Map |
| 2do4A | 1 | 0.5753 | 7.3 | 0.934 | Contact Map |
| 2djwA | 10 | 0.5205 | 6.7 | 0.935 | Contact Map |
| 2cq0A | 1 | 0.6027 | 5.8 | 0.937 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)