| 113_114 -force run |
| ID: | 1430412560 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 264 (264) | ||
| Sequences: | 215 (184) | ||
| Seq/Len: | 0.814 | ||
| Nf(neff/√len): | 11.3 |
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: 0.814).
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 |
| 13_A | 29_F | 2.787 | 1.00 |
| 92_T | 95_K | 2.256 | 0.97 |
| 9_V | 42_L | 2.211 | 0.97 |
| 38_A | 87_S | 2.203 | 0.97 |
| 60_I | 91_C | 1.983 | 0.93 |
| 13_A | 32_L | 1.962 | 0.93 |
| 56_L | 90_F | 1.949 | 0.92 |
| 210_I | 222_A | 1.949 | 0.92 |
| 225_L | 231_P | 1.947 | 0.92 |
| 4_K | 62_P | 1.897 | 0.91 |
| 212_N | 238_Y | 1.860 | 0.90 |
| 103_I | 148_V | 1.750 | 0.85 |
| 222_A | 232_F | 1.712 | 0.84 |
| 4_K | 10_Q | 1.696 | 0.83 |
| 3_V | 43_T | 1.594 | 0.77 |
| 173_A | 225_L | 1.584 | 0.77 |
| 26_F | 59_T | 1.579 | 0.76 |
| 5_T | 39_H | 1.554 | 0.75 |
| 3_V | 39_H | 1.544 | 0.74 |
| 210_I | 232_F | 1.534 | 0.73 |
| 218_S | 232_F | 1.512 | 0.72 |
| 11_S | 190_A | 1.510 | 0.72 |
| 56_L | 105_V | 1.464 | 0.68 |
| 224_I | 227_E | 1.457 | 0.68 |
| 3_V | 143_E | 1.433 | 0.66 |
| 218_S | 238_Y | 1.419 | 0.65 |
| 47_W | 122_G | 1.417 | 0.65 |
| 221_V | 232_F | 1.412 | 0.64 |
| 209_I | 233_I | 1.411 | 0.64 |
| 233_I | 263_V | 1.380 | 0.62 |
| 213_L | 225_L | 1.379 | 0.62 |
| 26_F | 29_F | 1.378 | 0.61 |
| 12_L | 55_V | 1.359 | 0.60 |
| 194_Q | 216_E | 1.357 | 0.60 |
| 90_F | 117_L | 1.348 | 0.59 |
| 182_E | 230_V | 1.341 | 0.58 |
| 24_E | 34_A | 1.337 | 0.58 |
| 225_L | 232_F | 1.336 | 0.58 |
| 138_R | 177_E | 1.330 | 0.57 |
| 6_L | 47_W | 1.325 | 0.57 |
| 4_K | 7_A | 1.302 | 0.55 |
| 173_A | 188_A | 1.296 | 0.54 |
| 212_N | 218_S | 1.292 | 0.54 |
| 5_T | 29_F | 1.284 | 0.53 |
| 224_I | 228_R | 1.273 | 0.52 |
| 92_T | 96_Y | 1.260 | 0.51 |
| 6_L | 130_R | 1.258 | 0.51 |
| 213_L | 217_P | 1.254 | 0.51 |
| 47_W | 148_V | 1.247 | 0.50 |
| 225_L | 228_R | 1.236 | 0.49 |
| 2_N | 43_T | 1.234 | 0.49 |
| 34_A | 95_K | 1.223 | 0.48 |
| 193_M | 216_E | 1.222 | 0.48 |
| 36_A | 40_D | 1.218 | 0.48 |
| 15_Q | 152_F | 1.214 | 0.47 |
| 87_S | 139_A | 1.214 | 0.47 |
| 36_A | 81_K | 1.214 | 0.47 |
| 55_V | 103_I | 1.209 | 0.47 |
| 42_L | 47_W | 1.208 | 0.47 |
| 117_L | 133_T | 1.206 | 0.47 |
| 190_A | 199_I | 1.200 | 0.46 |
| 5_T | 84_L | 1.197 | 0.46 |
| 54_E | 164_V | 1.192 | 0.45 |
| 121_G | 158_F | 1.191 | 0.45 |
| 70_V | 145_G | 1.189 | 0.45 |
| 223_D | 253_L | 1.181 | 0.44 |
| 187_A | 229_N | 1.175 | 0.44 |
| 86_L | 117_L | 1.169 | 0.43 |
| 232_F | 238_Y | 1.161 | 0.43 |
| 53_G | 75_P | 1.154 | 0.42 |
| 16_T | 65_V | 1.152 | 0.42 |
| 137_E | 141_A | 1.147 | 0.41 |
| 93_A | 135_L | 1.135 | 0.40 |
| 218_S | 225_L | 1.135 | 0.40 |
| 4_K | 59_T | 1.134 | 0.40 |
| 151_V | 155_S | 1.133 | 0.40 |
| 59_T | 62_P | 1.131 | 0.40 |
| 172_I | 175_L | 1.128 | 0.40 |
| 220_P | 231_P | 1.125 | 0.40 |
| 122_G | 125_V | 1.125 | 0.40 |
| 108_H | 118_Q | 1.124 | 0.40 |
| 173_A | 238_Y | 1.120 | 0.39 |
| 208_A | 225_L | 1.119 | 0.39 |
| 12_L | 241_K | 1.118 | 0.39 |
| 105_V | 247_Y | 1.118 | 0.39 |
| 221_V | 225_L | 1.111 | 0.38 |
| 103_I | 123_P | 1.109 | 0.38 |
| 2_N | 125_V | 1.107 | 0.38 |
| 231_P | 234_F | 1.106 | 0.38 |
| 2_N | 84_L | 1.105 | 0.38 |
| 177_E | 183_L | 1.101 | 0.38 |
| 31_S | 139_A | 1.100 | 0.38 |
| 4_K | 169_E | 1.099 | 0.37 |
| 208_A | 231_P | 1.097 | 0.37 |
| 47_W | 80_P | 1.096 | 0.37 |
| 4_K | 49_G | 1.088 | 0.37 |
| 168_E | 186_V | 1.085 | 0.36 |
| 213_L | 232_F | 1.081 | 0.36 |
| 180_L | 238_Y | 1.079 | 0.36 |
| 87_S | 92_T | 1.077 | 0.36 |
| 235_A | 255_F | 1.075 | 0.35 |
| 183_L | 261_E | 1.073 | 0.35 |
| 228_R | 231_P | 1.071 | 0.35 |
| 177_E | 234_F | 1.070 | 0.35 |
| 5_T | 160_I | 1.068 | 0.35 |
| 173_A | 208_A | 1.066 | 0.35 |
| 15_Q | 143_E | 1.064 | 0.35 |
| 176_I | 255_F | 1.055 | 0.34 |
| 88_M | 141_A | 1.055 | 0.34 |
| 89_A | 140_L | 1.050 | 0.33 |
| 173_A | 231_P | 1.049 | 0.33 |
| 173_A | 228_R | 1.049 | 0.33 |
| 103_I | 122_G | 1.046 | 0.33 |
| 229_N | 264_L | 1.046 | 0.33 |
| 220_P | 225_L | 1.045 | 0.33 |
| 74_P | 107_W | 1.043 | 0.33 |
| 10_Q | 13_A | 1.043 | 0.33 |
| 207_I | 214_D | 1.042 | 0.33 |
| 53_G | 57_H | 1.042 | 0.33 |
| 39_H | 52_L | 1.038 | 0.33 |
| 219_Y | 234_F | 1.036 | 0.32 |
| 39_H | 122_G | 1.033 | 0.32 |
| 173_A | 213_L | 1.033 | 0.32 |
| 214_D | 218_S | 1.031 | 0.32 |
| 237_G | 244_D | 1.025 | 0.32 |
| 29_F | 135_L | 1.022 | 0.31 |
| 93_A | 107_W | 1.019 | 0.31 |
| 88_M | 148_V | 1.019 | 0.31 |
| 92_T | 165_L | 1.017 | 0.31 |
| 138_R | 143_E | 1.014 | 0.31 |
| 15_Q | 105_V | 1.013 | 0.31 |
| 16_T | 29_F | 1.011 | 0.31 |
| 6_L | 59_T | 1.009 | 0.30 |
| 188_A | 225_L | 1.009 | 0.30 |
| 135_L | 215_G | 1.008 | 0.30 |
| 18_R | 29_F | 1.007 | 0.30 |
| 193_M | 200_A | 1.007 | 0.30 |
| 173_A | 217_P | 1.005 | 0.30 |
| 75_P | 164_V | 1.004 | 0.30 |
| 38_A | 79_R | 1.000 | 0.30 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 3cg4A | 1 | 0.3939 | 98.9 | 0.866 | Contact Map |
| 3cu5A | 2 | 0.3939 | 98.9 | 0.866 | Contact Map |
| 4le1A | 2 | 0.3939 | 98.9 | 0.868 | Contact Map |
| 2qxyA | 2 | 0.3939 | 98.9 | 0.868 | Contact Map |
| 3crnA | 2 | 0.3902 | 98.9 | 0.868 | Contact Map |
| 3cg0A | 4 | 0.3977 | 98.8 | 0.869 | Contact Map |
| 4ldzA | 2 | 0.4015 | 98.8 | 0.87 | Contact Map |
| 3c3mA | 1 | 0.3902 | 98.8 | 0.87 | Contact Map |
| 2qzjA | 6 | 0.3902 | 98.8 | 0.87 | Contact Map |
| 1w25A | 2 | 0.3939 | 98.8 | 0.871 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)