| bactin |
| ID: | 1432747809 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 375 (368) | ||
| Sequences: | 5930 (2905.9) | ||
| Seq/Len: | 16.114 | ||
| Nf(neff/√len): | 151.5 |
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: 16.114).
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 |
| 102_P | 130_P | 4.818 | 1.00 |
| 210_R | 214_E | 4.162 | 1.00 |
| 155_S | 303_T | 3.170 | 1.00 |
| 153_M | 274_I | 3.064 | 1.00 |
| 211_D | 215_K | 2.801 | 1.00 |
| 334_E | 337_Y | 2.796 | 1.00 |
| 155_S | 160_T | 2.710 | 1.00 |
| 66_T | 183_R | 2.651 | 1.00 |
| 278_T | 313_M | 2.643 | 1.00 |
| 312_R | 316_E | 2.532 | 1.00 |
| 303_T | 306_Y | 2.501 | 1.00 |
| 196_R | 254_R | 2.466 | 1.00 |
| 311_D | 315_K | 2.390 | 1.00 |
| 164_P | 281_S | 2.343 | 1.00 |
| 188_Y | 260_A | 2.304 | 1.00 |
| 314_Q | 328_K | 2.297 | 1.00 |
| 275_H | 316_E | 2.263 | 1.00 |
| 121_Q | 125_E | 2.255 | 1.00 |
| 151_I | 162_T | 2.215 | 1.00 |
| 12_N | 86_W | 2.195 | 1.00 |
| 359_K | 363_D | 2.110 | 1.00 |
| 177_R | 273_G | 1.989 | 1.00 |
| 102_P | 132_M | 1.955 | 1.00 |
| 220_A | 226_E | 1.947 | 1.00 |
| 107_E | 116_R | 1.925 | 1.00 |
| 305_M | 336_K | 1.925 | 1.00 |
| 83_E | 126_T | 1.916 | 1.00 |
| 310_A | 331_A | 1.912 | 1.00 |
| 55_G | 58_A | 1.881 | 1.00 |
| 20_G | 344_S | 1.879 | 1.00 |
| 337_Y | 341_I | 1.866 | 1.00 |
| 14_S | 158_G | 1.863 | 1.00 |
| 187_D | 191_K | 1.848 | 1.00 |
| 255_F | 303_T | 1.841 | 1.00 |
| 155_S | 309_I | 1.807 | 1.00 |
| 193_L | 248_I | 1.806 | 1.00 |
| 297_T | 317_I | 1.738 | 1.00 |
| 299_L | 313_M | 1.723 | 1.00 |
| 276_E | 280_N | 1.710 | 1.00 |
| 153_M | 162_T | 1.697 | 1.00 |
| 153_M | 160_T | 1.696 | 1.00 |
| 194_T | 203_T | 1.691 | 1.00 |
| 117_E | 121_Q | 1.690 | 1.00 |
| 148_T | 296_N | 1.678 | 1.00 |
| 123_M | 132_M | 1.676 | 1.00 |
| 87_H | 127_F | 1.666 | 1.00 |
| 209_V | 212_I | 1.660 | 1.00 |
| 164_P | 285_C | 1.659 | 1.00 |
| 9_V | 340_W | 1.644 | 1.00 |
| 135_A | 140_L | 1.643 | 1.00 |
| 251_G | 254_R | 1.641 | 1.00 |
| 17_C | 33_S | 1.637 | 1.00 |
| 189_L | 250_I | 1.623 | 1.00 |
| 188_Y | 264_P | 1.622 | 1.00 |
| 185_L | 257_C | 1.613 | 1.00 |
| 218_Y | 226_E | 1.604 | 1.00 |
| 313_M | 329_I | 1.604 | 1.00 |
| 23_G | 28_R | 1.595 | 1.00 |
| 105_L | 124_F | 1.571 | 1.00 |
| 262_F | 312_R | 1.564 | 1.00 |
| 7_A | 132_M | 1.545 | 1.00 |
| 142_L | 150_G | 1.543 | 1.00 |
| 334_E | 341_I | 1.522 | 1.00 |
| 56_D | 60_S | 1.517 | 1.00 |
| 190_M | 206_R | 1.516 | 1.00 |
| 102_P | 131_A | 1.514 | 1.00 |
| 154_D | 161_H | 1.494 | 1.00 |
| 19_A | 89_T | 1.477 | 1.00 |
| 192_I | 257_C | 1.477 | 1.00 |
| 310_A | 314_Q | 1.445 | 1.00 |
| 157_D | 183_R | 1.436 | 1.00 |
| 23_G | 344_S | 1.424 | 1.00 |
| 27_P | 341_I | 1.420 | 1.00 |
| 15_G | 157_D | 1.415 | 1.00 |
| 9_V | 343_G | 1.413 | 1.00 |
| 7_A | 347_A | 1.409 | 1.00 |
| 279_F | 316_E | 1.403 | 0.99 |
| 331_A | 335_R | 1.399 | 0.99 |
| 185_L | 261_L | 1.394 | 0.99 |
| 217_C | 258_P | 1.393 | 0.99 |
| 296_N | 330_I | 1.387 | 0.99 |
| 282_I | 294_Y | 1.385 | 0.99 |
| 308_G | 311_D | 1.380 | 0.99 |
| 124_F | 127_F | 1.376 | 0.99 |
| 174_A | 281_S | 1.367 | 0.99 |
| 24_D | 28_R | 1.342 | 0.99 |
| 357_I | 369_I | 1.338 | 0.99 |
| 162_T | 277_T | 1.336 | 0.99 |
| 87_H | 91_Y | 1.328 | 0.99 |
| 111_N | 115_N | 1.324 | 0.99 |
| 103_V | 123_M | 1.312 | 0.99 |
| 258_P | 306_Y | 1.308 | 0.99 |
| 78_N | 81_D | 1.307 | 0.99 |
| 20_G | 340_W | 1.305 | 0.99 |
| 285_C | 293_L | 1.305 | 0.99 |
| 196_R | 253_E | 1.292 | 0.99 |
| 7_A | 102_P | 1.292 | 0.99 |
| 153_M | 278_T | 1.290 | 0.99 |
| 106_T | 343_G | 1.277 | 0.99 |
| 353_Q | 356_W | 1.276 | 0.99 |
| 18_K | 30_V | 1.267 | 0.99 |
| 182_G | 303_T | 1.265 | 0.99 |
| 13_G | 302_G | 1.242 | 0.98 |
| 173_H | 281_S | 1.242 | 0.98 |
| 151_I | 278_T | 1.237 | 0.98 |
| 120_T | 134_V | 1.235 | 0.98 |
| 186_T | 213_K | 1.229 | 0.98 |
| 88_H | 92_N | 1.224 | 0.98 |
| 147_R | 298_V | 1.221 | 0.98 |
| 276_E | 279_F | 1.217 | 0.98 |
| 217_C | 306_Y | 1.216 | 0.98 |
| 180_L | 184_D | 1.201 | 0.98 |
| 192_I | 196_R | 1.201 | 0.98 |
| 182_G | 213_K | 1.200 | 0.98 |
| 222_D | 225_Q | 1.200 | 0.98 |
| 262_F | 308_G | 1.195 | 0.98 |
| 176_L | 284_K | 1.184 | 0.98 |
| 164_P | 174_A | 1.180 | 0.98 |
| 304_T | 331_A | 1.175 | 0.98 |
| 33_S | 37_R | 1.175 | 0.98 |
| 255_F | 306_Y | 1.173 | 0.98 |
| 299_L | 310_A | 1.170 | 0.97 |
| 314_Q | 329_I | 1.165 | 0.97 |
| 10_V | 103_V | 1.165 | 0.97 |
| 151_I | 164_P | 1.148 | 0.97 |
| 22_A | 27_P | 1.147 | 0.97 |
| 275_H | 312_R | 1.147 | 0.97 |
| 104_L | 343_G | 1.145 | 0.97 |
| 258_P | 262_F | 1.145 | 0.97 |
| 86_W | 119_M | 1.145 | 0.97 |
| 76_V | 79_W | 1.145 | 0.97 |
| 107_E | 111_N | 1.140 | 0.97 |
| 18_K | 340_W | 1.140 | 0.97 |
| 140_L | 343_G | 1.139 | 0.97 |
| 22_A | 347_A | 1.132 | 0.97 |
| 304_T | 309_I | 1.131 | 0.97 |
| 365_S | 369_I | 1.131 | 0.97 |
| 145_S | 338_S | 1.123 | 0.97 |
| 94_L | 97_A | 1.114 | 0.96 |
| 162_T | 278_T | 1.112 | 0.96 |
| 207_E | 210_R | 1.110 | 0.96 |
| 212_I | 217_C | 1.103 | 0.96 |
| 213_K | 216_L | 1.097 | 0.96 |
| 32_P | 35_V | 1.093 | 0.96 |
| 223_F | 227_M | 1.091 | 0.96 |
| 239_S | 247_V | 1.091 | 0.96 |
| 123_M | 129_T | 1.090 | 0.96 |
| 113_K | 117_E | 1.089 | 0.96 |
| 190_M | 209_V | 1.088 | 0.96 |
| 155_S | 274_I | 1.081 | 0.95 |
| 37_R | 81_D | 1.078 | 0.95 |
| 107_E | 136_I | 1.075 | 0.95 |
| 11_D | 14_S | 1.073 | 0.95 |
| 189_L | 209_V | 1.073 | 0.95 |
| 189_L | 192_I | 1.070 | 0.95 |
| 69_Y | 72_E | 1.068 | 0.95 |
| 344_S | 348_S | 1.066 | 0.95 |
| 17_C | 85_I | 1.065 | 0.95 |
| 67_L | 86_W | 1.060 | 0.95 |
| 155_S | 185_L | 1.059 | 0.95 |
| 136_I | 139_V | 1.058 | 0.95 |
| 133_Y | 346_L | 1.057 | 0.95 |
| 164_P | 294_Y | 1.054 | 0.95 |
| 259_E | 264_P | 1.053 | 0.95 |
| 112_P | 115_N | 1.049 | 0.94 |
| 341_I | 345_I | 1.047 | 0.94 |
| 188_Y | 191_K | 1.045 | 0.94 |
| 155_S | 304_T | 1.042 | 0.94 |
| 185_L | 303_T | 1.042 | 0.94 |
| 125_E | 130_P | 1.039 | 0.94 |
| 101_H | 130_P | 1.034 | 0.94 |
| 33_S | 40_H | 1.032 | 0.94 |
| 125_E | 132_M | 1.029 | 0.94 |
| 287_V | 290_R | 1.028 | 0.94 |
| 182_G | 186_T | 1.027 | 0.94 |
| 70_P | 73_H | 1.026 | 0.94 |
| 192_I | 254_R | 1.024 | 0.93 |
| 149_T | 289_I | 1.018 | 0.93 |
| 91_Y | 98_P | 1.016 | 0.93 |
| 304_T | 335_R | 1.015 | 0.93 |
| 281_S | 285_C | 1.012 | 0.93 |
| 197_G | 200_F | 1.010 | 0.93 |
| 135_A | 346_L | 1.010 | 0.93 |
| 73_H | 184_D | 1.009 | 0.93 |
| 354_Q | 360_Q | 1.009 | 0.93 |
| 262_F | 306_Y | 1.008 | 0.93 |
| 137_Q | 161_H | 1.007 | 0.93 |
| 208_I | 212_I | 1.006 | 0.93 |
| 272_C | 276_E | 1.006 | 0.93 |
| 109_P | 138_A | 1.005 | 0.93 |
| 16_M | 336_K | 1.003 | 0.93 |
| 52_S | 88_H | 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 | |
| 4pl7A | 2 | 0.9227 | 100 | 0.101 | Contact Map |
| 4am6A | 2 | 0.9947 | 100 | 0.114 | Contact Map |
| 4fo0A | 1 | 0.9733 | 100 | 0.12 | Contact Map |
| 3dwlA | 2 | 0.912 | 100 | 0.131 | Contact Map |
| 4b1yB | 1 | 0.9707 | 100 | 0.133 | Contact Map |
| 1k8kB | 1 | 0.4773 | 100 | 0.133 | Contact Map |
| 3qb0A | 4 | 0.976 | 100 | 0.134 | Contact Map |
| 1k8kA | 1 | 0.984 | 100 | 0.142 | Contact Map |
| 4i6mA | 1 | 0.952 | 100 | 0.153 | Contact Map |
| 4i6mB | 1 | 0.8907 | 100 | 0.161 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)