| 4G |
| ID: | 1488487759 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 160 (160) | ||
| Sequences: | 2717 (215.3) | ||
| Seq/Len: | 16.981 | ||
| Nf(neff/√len): | 17.0 |
HHblits Results: (2016_02)
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: 16.981).
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 |
| 129_G | 133_V | 2.416 | 1.00 |
| 153_Q | 156_E | 2.200 | 1.00 |
| 109_Q | 113_N | 2.034 | 1.00 |
| 3_F | 6_L | 1.959 | 1.00 |
| 141_C | 145_R | 1.950 | 1.00 |
| 65_R | 69_L | 1.913 | 1.00 |
| 156_E | 159_L | 1.860 | 1.00 |
| 2_V | 9_V | 1.700 | 1.00 |
| 150_R | 153_Q | 1.575 | 1.00 |
| 128_E | 133_V | 1.569 | 1.00 |
| 87_E | 90_G | 1.550 | 1.00 |
| 142_R | 145_R | 1.545 | 1.00 |
| 153_Q | 159_L | 1.516 | 1.00 |
| 117_S | 121_A | 1.495 | 1.00 |
| 54_N | 60_I | 1.491 | 1.00 |
| 36_G | 92_R | 1.464 | 1.00 |
| 146_H | 157_R | 1.450 | 1.00 |
| 148_P | 153_Q | 1.446 | 1.00 |
| 49_S | 52_L | 1.438 | 1.00 |
| 119_L | 122_T | 1.437 | 1.00 |
| 21_F | 25_L | 1.426 | 1.00 |
| 152_R | 156_E | 1.424 | 1.00 |
| 154_G | 159_L | 1.420 | 1.00 |
| 25_L | 36_G | 1.378 | 0.99 |
| 107_W | 114_S | 1.371 | 0.99 |
| 74_R | 77_D | 1.349 | 0.99 |
| 5_V | 11_R | 1.347 | 0.99 |
| 18_P | 21_F | 1.336 | 0.99 |
| 150_R | 156_E | 1.335 | 0.99 |
| 26_P | 30_G | 1.330 | 0.99 |
| 23_T | 26_P | 1.327 | 0.99 |
| 68_C | 71_S | 1.326 | 0.99 |
| 149_R | 153_Q | 1.316 | 0.99 |
| 92_R | 96_A | 1.316 | 0.99 |
| 121_A | 125_A | 1.315 | 0.99 |
| 140_A | 143_A | 1.273 | 0.99 |
| 62_D | 68_C | 1.268 | 0.99 |
| 18_P | 22_Q | 1.260 | 0.99 |
| 106_Y | 110_E | 1.246 | 0.98 |
| 36_G | 40_E | 1.245 | 0.98 |
| 129_G | 137_V | 1.238 | 0.98 |
| 112_K | 116_V | 1.234 | 0.98 |
| 67_L | 76_R | 1.226 | 0.98 |
| 128_E | 132_R | 1.222 | 0.98 |
| 79_L | 100_W | 1.218 | 0.98 |
| 107_W | 110_E | 1.208 | 0.98 |
| 22_Q | 26_P | 1.205 | 0.98 |
| 86_V | 90_G | 1.195 | 0.98 |
| 134_I | 137_V | 1.184 | 0.98 |
| 149_R | 152_R | 1.178 | 0.98 |
| 34_P | 39_E | 1.173 | 0.98 |
| 57_L | 65_R | 1.157 | 0.97 |
| 84_R | 89_L | 1.155 | 0.97 |
| 145_R | 150_R | 1.154 | 0.97 |
| 70_F | 74_R | 1.154 | 0.97 |
| 22_Q | 25_L | 1.149 | 0.97 |
| 105_Q | 129_G | 1.149 | 0.97 |
| 83_T | 86_V | 1.147 | 0.97 |
| 70_F | 77_D | 1.137 | 0.97 |
| 148_P | 152_R | 1.132 | 0.97 |
| 60_I | 79_L | 1.132 | 0.97 |
| 155_L | 158_I | 1.131 | 0.97 |
| 144_I | 148_P | 1.122 | 0.97 |
| 84_R | 87_E | 1.115 | 0.96 |
| 56_S | 60_I | 1.105 | 0.96 |
| 31_P | 36_G | 1.104 | 0.96 |
| 102_N | 105_Q | 1.101 | 0.96 |
| 111_L | 115_A | 1.093 | 0.96 |
| 148_P | 156_E | 1.092 | 0.96 |
| 115_A | 118_L | 1.086 | 0.96 |
| 147_I | 154_G | 1.079 | 0.95 |
| 138_Q | 142_R | 1.075 | 0.95 |
| 25_L | 30_G | 1.068 | 0.95 |
| 126_V | 129_G | 1.067 | 0.95 |
| 55_G | 63_D | 1.065 | 0.95 |
| 40_E | 88_L | 1.055 | 0.95 |
| 96_A | 113_N | 1.049 | 0.94 |
| 24_H | 50_I | 1.047 | 0.94 |
| 46_R | 62_D | 1.047 | 0.94 |
| 151_I | 154_G | 1.046 | 0.94 |
| 3_F | 10_N | 1.045 | 0.94 |
| 100_W | 116_V | 1.043 | 0.94 |
| 92_R | 95_E | 1.036 | 0.94 |
| 152_R | 159_L | 1.031 | 0.94 |
| 102_N | 109_Q | 1.030 | 0.94 |
| 4_A | 10_N | 1.023 | 0.93 |
| 97_L | 104_L | 1.021 | 0.93 |
| 59_L | 62_D | 1.015 | 0.93 |
| 86_V | 89_L | 1.011 | 0.93 |
| 60_I | 78_L | 1.007 | 0.93 |
| 102_N | 112_K | 1.004 | 0.93 |
| 35_E | 50_I | 1.002 | 0.92 |
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 | |
| 2mg1A | 1 | 0.0688 | 31.4 | 0.943 | Contact Map |
| 2vyoA | 1 | 0.1812 | 2.8 | 0.965 | Contact Map |
| 3dl8E | 2 | 0.0813 | 2.7 | 0.965 | Contact Map |
| 2qfaC | 1 | 0.2812 | 2.2 | 0.967 | Contact Map |
| 5a1uC | 1 | 0 | 2.1 | 0.967 | Contact Map |
| 1is8A | 10 | 0.3875 | 1.2 | 0.971 | Contact Map |
| 4u9rA | 1 | 0 | 1.1 | 0.972 | Contact Map |
| 3libA | 10 | 0.4 | 1.1 | 0.972 | Contact Map |
| 3b0zB | 1 | 0.0875 | 1 | 0.973 | Contact Map |
| 2c46A | 4 | 0.2188 | 1 | 0.973 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)