| T0786 -force run |
| ID: | 1402363018 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 264 (253) | ||
| Sequences: | 117 (94.5) | ||
| Seq/Len: | 0.462 | ||
| Nf(neff/√len): | 5.9 |
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: 0.462).
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 |
| 105_I | 128_M | 2.798 | 0.98 |
| 85_I | 185_I | 2.476 | 0.96 |
| 73_I | 81_M | 2.223 | 0.91 |
| 57_D | 129_K | 1.937 | 0.81 |
| 82_R | 183_N | 1.791 | 0.74 |
| 117_S | 193_L | 1.727 | 0.70 |
| 47_W | 61_T | 1.664 | 0.66 |
| 105_I | 133_Y | 1.612 | 0.62 |
| 59_F | 95_L | 1.611 | 0.62 |
| 145_V | 244_K | 1.609 | 0.62 |
| 147_V | 224_V | 1.606 | 0.62 |
| 33_E | 79_E | 1.510 | 0.55 |
| 200_C | 222_F | 1.492 | 0.53 |
| 35_L | 48_L | 1.478 | 0.52 |
| 44_S | 67_D | 1.476 | 0.52 |
| 19_S | 62_V | 1.460 | 0.51 |
| 86_R | 179_D | 1.445 | 0.50 |
| 172_I | 216_C | 1.439 | 0.49 |
| 13_G | 227_L | 1.424 | 0.48 |
| 66_T | 133_Y | 1.415 | 0.47 |
| 54_T | 227_L | 1.401 | 0.46 |
| 96_Q | 209_Y | 1.393 | 0.46 |
| 118_L | 134_L | 1.382 | 0.45 |
| 32_R | 88_S | 1.377 | 0.45 |
| 46_I | 212_E | 1.374 | 0.44 |
| 107_Y | 147_V | 1.353 | 0.43 |
| 69_C | 227_L | 1.342 | 0.42 |
| 87_F | 186_Q | 1.339 | 0.42 |
| 85_I | 89_I | 1.328 | 0.41 |
| 54_T | 107_Y | 1.328 | 0.41 |
| 5_Q | 234_P | 1.324 | 0.41 |
| 52_F | 170_I | 1.324 | 0.41 |
| 108_K | 123_M | 1.323 | 0.41 |
| 103_S | 132_N | 1.313 | 0.40 |
| 44_S | 80_H | 1.302 | 0.39 |
| 39_L | 155_L | 1.300 | 0.39 |
| 128_M | 133_Y | 1.297 | 0.39 |
| 170_I | 183_N | 1.292 | 0.38 |
| 100_E | 129_K | 1.290 | 0.38 |
| 239_K | 246_Q | 1.280 | 0.38 |
| 118_L | 133_Y | 1.277 | 0.37 |
| 66_T | 134_L | 1.271 | 0.37 |
| 47_W | 251_F | 1.271 | 0.37 |
| 39_L | 101_F | 1.255 | 0.36 |
| 13_G | 45_I | 1.253 | 0.36 |
| 84_L | 150_N | 1.236 | 0.34 |
| 5_Q | 61_T | 1.230 | 0.34 |
| 107_Y | 119_H | 1.226 | 0.34 |
| 69_C | 237_S | 1.225 | 0.34 |
| 66_T | 121_A | 1.222 | 0.34 |
| 113_F | 201_S | 1.218 | 0.33 |
| 55_L | 64_I | 1.214 | 0.33 |
| 84_L | 106_L | 1.213 | 0.33 |
| 156_N | 185_I | 1.210 | 0.33 |
| 9_L | 119_H | 1.200 | 0.32 |
| 19_S | 185_I | 1.184 | 0.31 |
| 18_E | 22_N | 1.182 | 0.31 |
| 146_I | 149_K | 1.181 | 0.31 |
| 54_T | 118_L | 1.180 | 0.31 |
| 69_C | 199_G | 1.177 | 0.31 |
| 58_T | 107_Y | 1.174 | 0.30 |
| 38_I | 205_L | 1.170 | 0.30 |
| 58_T | 147_V | 1.170 | 0.30 |
| 93_L | 110_H | 1.167 | 0.30 |
| 36_T | 48_L | 1.160 | 0.29 |
| 32_R | 168_F | 1.160 | 0.29 |
| 71_D | 121_A | 1.156 | 0.29 |
| 80_H | 182_A | 1.153 | 0.29 |
| 85_I | 88_S | 1.147 | 0.29 |
| 126_I | 227_L | 1.146 | 0.29 |
| 118_L | 163_I | 1.143 | 0.28 |
| 6_L | 235_Q | 1.143 | 0.28 |
| 19_S | 37_D | 1.141 | 0.28 |
| 192_I | 223_V | 1.137 | 0.28 |
| 89_I | 93_L | 1.133 | 0.28 |
| 45_I | 62_V | 1.133 | 0.28 |
| 73_I | 82_R | 1.127 | 0.27 |
| 66_T | 72_H | 1.118 | 0.27 |
| 49_K | 123_M | 1.118 | 0.27 |
| 92_W | 115_G | 1.118 | 0.27 |
| 155_L | 188_T | 1.117 | 0.27 |
| 87_F | 123_M | 1.114 | 0.27 |
| 21_R | 63_L | 1.107 | 0.26 |
| 196_F | 201_S | 1.105 | 0.26 |
| 126_I | 175_I | 1.100 | 0.26 |
| 13_G | 49_K | 1.098 | 0.26 |
| 51_K | 225_S | 1.098 | 0.26 |
| 67_D | 101_F | 1.096 | 0.26 |
| 181_L | 185_I | 1.093 | 0.25 |
| 181_L | 196_F | 1.090 | 0.25 |
| 103_S | 235_Q | 1.087 | 0.25 |
| 37_D | 62_V | 1.087 | 0.25 |
| 133_Y | 227_L | 1.086 | 0.25 |
| 88_S | 123_M | 1.085 | 0.25 |
| 118_L | 227_L | 1.085 | 0.25 |
| 95_L | 236_V | 1.084 | 0.25 |
| 131_V | 157_I | 1.083 | 0.25 |
| 13_G | 88_S | 1.082 | 0.25 |
| 81_M | 227_L | 1.079 | 0.25 |
| 13_G | 69_C | 1.071 | 0.24 |
| 74_A | 103_S | 1.070 | 0.24 |
| 49_K | 59_F | 1.068 | 0.24 |
| 40_A | 168_F | 1.067 | 0.24 |
| 66_T | 71_D | 1.065 | 0.24 |
| 178_I | 219_V | 1.063 | 0.24 |
| 47_W | 91_H | 1.061 | 0.24 |
| 195_D | 250_Y | 1.061 | 0.24 |
| 85_I | 181_L | 1.060 | 0.24 |
| 5_Q | 81_M | 1.058 | 0.24 |
| 40_A | 98_N | 1.057 | 0.23 |
| 72_H | 81_M | 1.045 | 0.23 |
| 71_D | 74_A | 1.043 | 0.23 |
| 54_T | 149_K | 1.043 | 0.23 |
| 61_T | 234_P | 1.043 | 0.23 |
| 118_L | 199_G | 1.042 | 0.23 |
| 54_T | 224_V | 1.040 | 0.23 |
| 42_E | 108_K | 1.037 | 0.22 |
| 51_K | 112_P | 1.037 | 0.22 |
| 156_N | 169_N | 1.036 | 0.22 |
| 47_W | 141_N | 1.035 | 0.22 |
| 149_K | 154_E | 1.029 | 0.22 |
| 39_L | 154_E | 1.029 | 0.22 |
| 69_C | 118_L | 1.027 | 0.22 |
| 142_F | 159_D | 1.025 | 0.22 |
| 72_H | 126_I | 1.024 | 0.22 |
| 103_S | 125_I | 1.023 | 0.22 |
| 45_I | 72_H | 1.023 | 0.22 |
| 41_T | 71_D | 1.019 | 0.21 |
| 36_T | 62_V | 1.014 | 0.21 |
| 131_V | 168_F | 1.012 | 0.21 |
| 44_S | 147_V | 1.012 | 0.21 |
| 42_E | 178_I | 1.011 | 0.21 |
| 52_F | 71_D | 1.010 | 0.21 |
| 163_I | 215_I | 1.009 | 0.21 |
| 181_L | 219_V | 1.007 | 0.21 |
| 49_K | 62_V | 1.007 | 0.21 |
| 78_E | 243_V | 1.007 | 0.21 |
| 91_H | 227_L | 1.005 | 0.21 |
| 182_A | 225_S | 1.003 | 0.21 |
| 200_C | 215_I | 1.003 | 0.21 |
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 | |
| 4qvuA | 1 | 0.822 | 100 | 0.613 | Contact Map |
| 1gupA | 4 | 0.9432 | 100 | 0.738 | Contact Map |
| 1z84A | 2 | 0.8826 | 100 | 0.769 | Contact Map |
| 4i5tA | 2 | 0.8864 | 100 | 0.782 | Contact Map |
| 3imiA | 4 | 0.5303 | 99 | 0.904 | Contact Map |
| 1y23A | 5 | 0.5227 | 98.9 | 0.911 | Contact Map |
| 3o0mA | 2 | 0.5114 | 98.8 | 0.913 | Contact Map |
| 4incA | 2 | 0.4015 | 98.8 | 0.913 | Contact Map |
| 3o1cA | 1 | 0.4129 | 98.8 | 0.914 | Contact Map |
| 3r6fA | 1 | 0.4886 | 98.7 | 0.917 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)