| Ymic coli - TPR wolbachia - Ycim Paludibacter all trimmed |
| ID: | 1489142878 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 311 (307) | ||
| Sequences: | 46884 (34342.3) | ||
| Seq/Len: | 152.717 | ||
| Nf(neff/√len): | 1960.0 |
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: 152.717).
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 |
| 117_E | 120_K | 3.360 | 1.00 |
| 190_E | 193_K | 3.299 | 1.00 |
| 156_D | 159_R | 3.271 | 1.00 |
| 225_K | 228_E | 3.179 | 1.00 |
| 45_E | 48_R | 3.044 | 1.00 |
| 83_L | 86_R | 2.986 | 1.00 |
| 11_Q | 14_K | 2.951 | 1.00 |
| 258_G | 261_A | 2.879 | 1.00 |
| 305_M | 308_E | 2.419 | 1.00 |
| 33_H | 52_I | 2.379 | 1.00 |
| 71_I | 90_M | 2.359 | 1.00 |
| 182_G | 198_L | 2.229 | 1.00 |
| 109_L | 125_A | 2.172 | 1.00 |
| 75_G | 91_F | 2.150 | 1.00 |
| 148_A | 164_L | 2.104 | 1.00 |
| 74_L | 90_M | 2.083 | 1.00 |
| 105_L | 124_V | 2.067 | 1.00 |
| 178_S | 197_S | 2.055 | 1.00 |
| 36_L | 52_I | 2.032 | 1.00 |
| 212_T | 232_F | 1.999 | 1.00 |
| 92_N | 108_L | 1.958 | 1.00 |
| 216_L | 232_F | 1.954 | 1.00 |
| 217_Q | 233_L | 1.931 | 1.00 |
| 20_L | 36_L | 1.905 | 1.00 |
| 108_L | 124_V | 1.902 | 1.00 |
| 181_M | 197_S | 1.875 | 1.00 |
| 144_Y | 163_L | 1.867 | 1.00 |
| 91_F | 107_Q | 1.821 | 1.00 |
| 199_Q | 216_L | 1.817 | 1.00 |
| 165_K | 181_M | 1.770 | 1.00 |
| 147_L | 163_L | 1.740 | 1.00 |
| 195_V | 199_Q | 1.709 | 1.00 |
| 230_A | 234_Q | 1.689 | 1.00 |
| 88_E | 92_N | 1.683 | 1.00 |
| 16_V | 20_L | 1.677 | 1.00 |
| 161_M | 165_K | 1.675 | 1.00 |
| 58_E | 74_L | 1.672 | 1.00 |
| 234_Q | 249_L | 1.641 | 1.00 |
| 78_Y | 90_M | 1.629 | 1.00 |
| 220_Y | 232_F | 1.620 | 1.00 |
| 36_L | 40_F | 1.612 | 1.00 |
| 40_F | 52_I | 1.599 | 1.00 |
| 185_F | 197_S | 1.579 | 1.00 |
| 246_E | 265_Y | 1.577 | 1.00 |
| 112_Y | 124_V | 1.545 | 1.00 |
| 19_F | 35_T | 1.539 | 1.00 |
| 40_F | 48_R | 1.538 | 1.00 |
| 112_Y | 120_K | 1.525 | 1.00 |
| 151_H | 159_R | 1.519 | 1.00 |
| 220_Y | 228_E | 1.512 | 1.00 |
| 122_I | 126_E | 1.503 | 1.00 |
| 3_G | 19_F | 1.498 | 1.00 |
| 164_L | 180_M | 1.483 | 1.00 |
| 37_G | 57_M | 1.480 | 1.00 |
| 126_E | 147_L | 1.471 | 1.00 |
| 198_L | 215_M | 1.460 | 1.00 |
| 185_F | 190_E | 1.454 | 1.00 |
| 74_L | 78_Y | 1.431 | 1.00 |
| 78_Y | 86_R | 1.426 | 1.00 |
| 105_L | 127_R | 1.407 | 0.99 |
| 183_R | 215_M | 1.384 | 0.99 |
| 185_F | 193_K | 1.382 | 0.99 |
| 151_H | 163_L | 1.380 | 0.99 |
| 108_L | 112_Y | 1.368 | 0.99 |
| 195_V | 223_L | 1.342 | 0.99 |
| 249_L | 253_I | 1.342 | 0.99 |
| 159_R | 162_T | 1.338 | 0.99 |
| 216_L | 220_Y | 1.336 | 0.99 |
| 78_Y | 83_L | 1.335 | 0.99 |
| 220_Y | 225_K | 1.334 | 0.99 |
| 125_A | 146_E | 1.315 | 0.99 |
| 151_H | 156_D | 1.312 | 0.99 |
| 181_M | 185_F | 1.311 | 0.99 |
| 86_R | 89_D | 1.302 | 0.99 |
| 40_F | 45_E | 1.293 | 0.99 |
| 167_G | 177_V | 1.292 | 0.99 |
| 57_M | 73_Q | 1.275 | 0.99 |
| 112_Y | 117_E | 1.268 | 0.99 |
| 94_L | 104_A | 1.255 | 0.99 |
| 233_L | 248_M | 1.253 | 0.99 |
| 201_V | 211_E | 1.246 | 0.98 |
| 250_A | 266_I | 1.245 | 0.98 |
| 71_I | 93_Q | 1.245 | 0.98 |
| 193_K | 196_E | 1.244 | 0.98 |
| 16_V | 40_F | 1.243 | 0.98 |
| 228_E | 231_E | 1.240 | 0.98 |
| 230_A | 249_L | 1.234 | 0.98 |
| 6_F | 14_K | 1.231 | 0.98 |
| 48_R | 51_R | 1.228 | 0.98 |
| 263_Q | 267_T | 1.214 | 0.98 |
| 88_E | 112_Y | 1.202 | 0.98 |
| 161_M | 185_F | 1.202 | 0.98 |
| 147_L | 151_H | 1.201 | 0.98 |
| 6_F | 11_Q | 1.200 | 0.98 |
| 120_K | 123_D | 1.195 | 0.98 |
| 179_I | 215_M | 1.189 | 0.98 |
| 253_I | 258_G | 1.187 | 0.98 |
| 50_I | 81_A | 1.184 | 0.98 |
| 6_F | 18_L | 1.182 | 0.98 |
| 88_E | 115_T | 1.175 | 0.98 |
| 23_L | 33_H | 1.172 | 0.98 |
| 23_L | 32_A | 1.169 | 0.97 |
| 38_N | 73_Q | 1.160 | 0.97 |
| 195_V | 220_Y | 1.156 | 0.97 |
| 50_I | 78_Y | 1.149 | 0.97 |
| 281_K | 284_D | 1.147 | 0.97 |
| 195_V | 219_C | 1.144 | 0.97 |
| 16_V | 36_L | 1.143 | 0.97 |
| 161_M | 188_K | 1.142 | 0.97 |
| 72_Q | 107_Q | 1.131 | 0.97 |
| 13_D | 43_R | 1.129 | 0.97 |
| 5_N | 9_S | 1.128 | 0.97 |
| 212_T | 235_R | 1.126 | 0.97 |
| 230_A | 256_R | 1.123 | 0.97 |
| 276_M | 280_H | 1.119 | 0.96 |
| 145_C | 180_M | 1.113 | 0.96 |
| 200_R | 204_Q | 1.112 | 0.96 |
| 261_A | 264_V | 1.104 | 0.96 |
| 217_Q | 236_A | 1.099 | 0.96 |
| 16_V | 43_R | 1.098 | 0.96 |
| 88_E | 108_L | 1.091 | 0.96 |
| 34_L | 73_Q | 1.088 | 0.96 |
| 217_Q | 229_W | 1.082 | 0.96 |
| 47_D | 81_A | 1.081 | 0.95 |
| 72_Q | 104_A | 1.078 | 0.95 |
| 179_I | 211_E | 1.075 | 0.95 |
| 280_H | 296_K | 1.075 | 0.95 |
| 253_I | 261_A | 1.072 | 0.95 |
| 76_R | 107_Q | 1.068 | 0.95 |
| 85_D | 115_T | 1.059 | 0.95 |
| 22_M | 32_A | 1.055 | 0.95 |
| 178_S | 200_R | 1.050 | 0.94 |
| 178_S | 201_V | 1.049 | 0.94 |
| 14_K | 17_D | 1.047 | 0.94 |
| 71_I | 94_L | 1.045 | 0.94 |
| 300_M | 305_M | 1.041 | 0.94 |
| 50_I | 74_L | 1.041 | 0.94 |
| 230_A | 252_I | 1.040 | 0.94 |
| 235_R | 239_E | 1.040 | 0.94 |
| 46_V | 77_D | 1.038 | 0.94 |
| 88_E | 111_I | 1.036 | 0.94 |
| 77_D | 81_A | 1.035 | 0.94 |
| 161_M | 184_V | 1.029 | 0.94 |
| 127_R | 131_L | 1.028 | 0.94 |
| 191_Y | 223_L | 1.027 | 0.94 |
| 18_L | 22_M | 1.021 | 0.93 |
| 148_A | 167_G | 1.015 | 0.93 |
| 145_C | 177_V | 1.015 | 0.93 |
| 286_H | 289_E | 1.015 | 0.93 |
| 195_V | 216_L | 1.008 | 0.93 |
| 218_T | 248_M | 1.008 | 0.93 |
| 109_L | 128_L | 1.006 | 0.93 |
| 158_D | 188_K | 1.006 | 0.93 |
| 149_L | 180_M | 1.006 | 0.93 |
| 34_L | 70_A | 1.004 | 0.93 |
| 253_I | 265_Y | 1.001 | 0.92 |
| 182_G | 194_A | 1.001 | 0.92 |
| 144_Y | 166_K | 1.000 | 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 | |
| 1w3bA | 2 | 0.9678 | 100 | -0.009 | Contact Map |
| 4ui9J | 1 | 0 | 100 | 0.052 | Contact Map |
| 4ui9C | 2 | 0 | 100 | 0.083 | Contact Map |
| 4rg9A | 2 | 0.8232 | 100 | 0.086 | Contact Map |
| 2y4tA | 3 | 0.926 | 100 | 0.088 | Contact Map |
| 4ui9F | 2 | 0 | 100 | 0.089 | Contact Map |
| 2xpiA | 2 | 0.9228 | 100 | 0.097 | Contact Map |
| 4ui9X | 2 | 0 | 100 | 0.1 | Contact Map |
| 3fp2A | 1 | 0.955 | 100 | 0.102 | Contact Map |
| 4g1tA | 2 | 0.955 | 100 | 0.108 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)