| ecoli_RtcB |
| ID: | 1430162541 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 408 (401) | ||
| Sequences: | 923 (629.5) | ||
| Seq/Len: | 2.302 | ||
| Nf(neff/√len): | 31.4 |
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: 2.302).
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 |
| 347_K | 350_K | 3.523 | 1.00 |
| 186_S | 250_M | 3.120 | 1.00 |
| 169_F | 313_P | 3.111 | 1.00 |
| 64_K | 292_E | 3.039 | 1.00 |
| 288_Q | 293_E | 3.025 | 1.00 |
| 347_K | 351_L | 2.974 | 1.00 |
| 324_R | 395_E | 2.726 | 1.00 |
| 23_E | 26_A | 2.674 | 1.00 |
| 82_A | 322_I | 2.671 | 1.00 |
| 193_N | 197_T | 2.529 | 1.00 |
| 26_A | 49_V | 2.519 | 1.00 |
| 39_I | 43_I | 2.378 | 1.00 |
| 182_I | 254_V | 2.326 | 1.00 |
| 30_L | 45_V | 2.313 | 1.00 |
| 103_I | 170_I | 2.303 | 1.00 |
| 45_V | 49_V | 2.073 | 0.99 |
| 315_S | 318_A | 2.028 | 0.99 |
| 89_A | 174_L | 2.012 | 0.99 |
| 174_L | 403_V | 2.011 | 0.99 |
| 180_V | 403_V | 1.996 | 0.99 |
| 346_T | 350_K | 1.980 | 0.99 |
| 107_V | 254_V | 1.931 | 0.99 |
| 190_G | 193_N | 1.894 | 0.99 |
| 81_N | 278_N | 1.890 | 0.99 |
| 354_V | 373_I | 1.853 | 0.99 |
| 303_S | 308_Q | 1.851 | 0.99 |
| 343_M | 348_A | 1.849 | 0.99 |
| 311_I | 322_I | 1.840 | 0.98 |
| 319_K | 399_T | 1.809 | 0.98 |
| 30_L | 43_I | 1.768 | 0.98 |
| 106_A | 257_A | 1.763 | 0.98 |
| 195_I | 239_A | 1.746 | 0.98 |
| 326_L | 395_E | 1.736 | 0.98 |
| 57_I | 72_V | 1.734 | 0.98 |
| 103_I | 254_V | 1.674 | 0.97 |
| 67_I | 233_L | 1.673 | 0.97 |
| 361_T | 405_C | 1.653 | 0.96 |
| 210_T | 223_M | 1.648 | 0.96 |
| 79_G | 247_R | 1.629 | 0.96 |
| 309_Y | 324_R | 1.629 | 0.96 |
| 82_A | 181_W | 1.617 | 0.96 |
| 324_R | 397_I | 1.588 | 0.95 |
| 83_L | 251_M | 1.579 | 0.95 |
| 163_L | 170_I | 1.571 | 0.95 |
| 352_F | 376_I | 1.567 | 0.95 |
| 335_C | 394_V | 1.567 | 0.95 |
| 226_T | 229_F | 1.560 | 0.95 |
| 102_A | 260_S | 1.548 | 0.94 |
| 227_E | 231_D | 1.535 | 0.94 |
| 89_A | 93_P | 1.533 | 0.94 |
| 383_I | 387_M | 1.518 | 0.93 |
| 77_G | 244_S | 1.507 | 0.93 |
| 25_D | 347_K | 1.504 | 0.93 |
| 206_E | 228_Y | 1.502 | 0.93 |
| 286_K | 293_E | 1.491 | 0.93 |
| 100_R | 404_V | 1.478 | 0.92 |
| 318_A | 321_F | 1.454 | 0.91 |
| 13_V | 30_L | 1.451 | 0.91 |
| 83_L | 184_L | 1.451 | 0.91 |
| 88_T | 179_Q | 1.449 | 0.91 |
| 209_E | 228_Y | 1.426 | 0.90 |
| 352_F | 378_M | 1.420 | 0.90 |
| 225_G | 230_D | 1.418 | 0.90 |
| 56_T | 59_S | 1.417 | 0.90 |
| 203_A | 222_F | 1.403 | 0.89 |
| 174_L | 401_R | 1.394 | 0.89 |
| 173_C | 183_M | 1.393 | 0.89 |
| 236_V | 284_V | 1.387 | 0.89 |
| 382_D | 385_A | 1.380 | 0.88 |
| 304_A | 327_G | 1.378 | 0.88 |
| 89_A | 178_D | 1.362 | 0.87 |
| 30_L | 49_V | 1.359 | 0.87 |
| 84_R | 275_E | 1.344 | 0.87 |
| 224_E | 295_Y | 1.327 | 0.86 |
| 90_E | 178_D | 1.322 | 0.85 |
| 42_H | 290_F | 1.316 | 0.85 |
| 321_F | 383_I | 1.315 | 0.85 |
| 15_M | 22_V | 1.308 | 0.84 |
| 107_V | 257_A | 1.293 | 0.84 |
| 33_T | 55_S | 1.291 | 0.83 |
| 56_T | 297_T | 1.281 | 0.83 |
| 33_T | 43_I | 1.281 | 0.83 |
| 40_F | 294_I | 1.280 | 0.83 |
| 54_G | 219_L | 1.277 | 0.82 |
| 206_E | 210_T | 1.267 | 0.82 |
| 18_K | 385_A | 1.267 | 0.82 |
| 32_N | 216_S | 1.258 | 0.81 |
| 280_H | 283_Y | 1.245 | 0.80 |
| 92_L | 266_V | 1.243 | 0.80 |
| 336_S | 390_Q | 1.237 | 0.80 |
| 59_S | 297_T | 1.233 | 0.79 |
| 62_P | 296_V | 1.231 | 0.79 |
| 224_E | 233_L | 1.215 | 0.78 |
| 371_E | 376_I | 1.209 | 0.77 |
| 360_A | 378_M | 1.202 | 0.77 |
| 108_P | 163_L | 1.197 | 0.76 |
| 310_G | 323_V | 1.192 | 0.76 |
| 102_A | 105_T | 1.191 | 0.76 |
| 174_L | 178_D | 1.191 | 0.76 |
| 19_G | 22_V | 1.188 | 0.76 |
| 52_G | 73_G | 1.188 | 0.76 |
| 77_G | 283_Y | 1.188 | 0.76 |
| 85_T | 180_V | 1.186 | 0.76 |
| 255_V | 258_L | 1.183 | 0.75 |
| 33_T | 71_A | 1.182 | 0.75 |
| 314_G | 320_S | 1.171 | 0.74 |
| 141_Y | 175_D | 1.159 | 0.73 |
| 38_F | 68_I | 1.153 | 0.73 |
| 100_R | 104_E | 1.150 | 0.72 |
| 170_I | 254_V | 1.148 | 0.72 |
| 109_H | 159_H | 1.148 | 0.72 |
| 84_R | 179_Q | 1.144 | 0.72 |
| 55_S | 71_A | 1.144 | 0.72 |
| 38_F | 65_G | 1.137 | 0.71 |
| 233_L | 295_Y | 1.136 | 0.71 |
| 285_Q | 303_S | 1.135 | 0.71 |
| 314_G | 383_I | 1.134 | 0.71 |
| 77_G | 280_H | 1.128 | 0.70 |
| 50_H | 73_G | 1.126 | 0.70 |
| 69_P | 169_F | 1.123 | 0.70 |
| 184_L | 233_L | 1.119 | 0.69 |
| 385_A | 388_A | 1.111 | 0.69 |
| 141_Y | 162_T | 1.109 | 0.68 |
| 284_V | 405_C | 1.108 | 0.68 |
| 309_Y | 397_I | 1.107 | 0.68 |
| 259_Q | 364_V | 1.105 | 0.68 |
| 40_F | 292_E | 1.102 | 0.68 |
| 314_G | 317_G | 1.097 | 0.67 |
| 341_R | 345_R | 1.096 | 0.67 |
| 244_S | 248_D | 1.094 | 0.67 |
| 107_V | 250_M | 1.093 | 0.67 |
| 229_F | 302_V | 1.091 | 0.66 |
| 375_E | 380_Y | 1.086 | 0.66 |
| 55_S | 59_S | 1.076 | 0.65 |
| 206_E | 209_E | 1.075 | 0.65 |
| 182_I | 258_L | 1.074 | 0.65 |
| 298_R | 334_S | 1.071 | 0.64 |
| 58_G | 73_G | 1.070 | 0.64 |
| 97_A | 101_Q | 1.068 | 0.64 |
| 65_G | 235_A | 1.066 | 0.64 |
| 49_V | 335_C | 1.065 | 0.64 |
| 384_D | 387_M | 1.062 | 0.63 |
| 13_V | 43_I | 1.060 | 0.63 |
| 305_R | 308_Q | 1.059 | 0.63 |
| 212_E | 221_Y | 1.057 | 0.63 |
| 25_D | 28_Q | 1.055 | 0.63 |
| 202_L | 228_Y | 1.050 | 0.62 |
| 53_K | 193_N | 1.050 | 0.62 |
| 140_G | 145_T | 1.045 | 0.62 |
| 155_N | 194_A | 1.044 | 0.61 |
| 77_G | 240_Q | 1.041 | 0.61 |
| 305_R | 333_C | 1.041 | 0.61 |
| 307_G | 324_R | 1.040 | 0.61 |
| 184_L | 247_R | 1.038 | 0.61 |
| 169_F | 242_F | 1.038 | 0.61 |
| 121_G | 130_V | 1.036 | 0.61 |
| 287_E | 296_V | 1.034 | 0.60 |
| 319_K | 361_T | 1.033 | 0.60 |
| 25_D | 51_L | 1.033 | 0.60 |
| 53_K | 74_V | 1.032 | 0.60 |
| 356_D | 360_A | 1.030 | 0.60 |
| 26_A | 30_L | 1.028 | 0.60 |
| 184_L | 251_M | 1.028 | 0.60 |
| 86_A | 179_Q | 1.026 | 0.59 |
| 315_S | 371_E | 1.018 | 0.59 |
| 77_G | 186_S | 1.015 | 0.58 |
| 142_Q | 145_T | 1.014 | 0.58 |
| 35_K | 227_E | 1.014 | 0.58 |
| 233_L | 237_A | 1.014 | 0.58 |
| 187_G | 300_G | 1.013 | 0.58 |
| 60_V | 386_V | 1.010 | 0.58 |
| 99_L | 172_I | 1.009 | 0.58 |
| 344_S | 348_A | 1.009 | 0.58 |
| 227_E | 329_E | 1.008 | 0.57 |
| 199_F | 235_A | 1.008 | 0.57 |
| 121_G | 137_L | 1.007 | 0.57 |
| 250_M | 254_V | 1.007 | 0.57 |
| 82_A | 183_M | 1.006 | 0.57 |
| 353_S | 356_D | 1.006 | 0.57 |
| 388_A | 396_V | 1.005 | 0.57 |
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 | |
| 2epgA | 2 | 0.9093 | 100 | 0.099 | Contact Map |
| 4dwrB | 3 | 0.9853 | 100 | 0.102 | Contact Map |
| 1pbyA | 1 | 0.1789 | 27.7 | 0.977 | Contact Map |
| 2wasA | 3 | 0.2672 | 21 | 0.978 | Contact Map |
| 2b78A | 1 | 0.299 | 19.3 | 0.979 | Contact Map |
| 1w2lA | 1 | 0.1985 | 15.3 | 0.98 | Contact Map |
| 3c0kA | 2 | 0.3015 | 15 | 0.98 | Contact Map |
| 4o9uB | 2 | 0.2279 | 13.6 | 0.98 | Contact Map |
| 3vseA | 4 | 0.3064 | 12.8 | 0.98 | Contact Map |
| 4j1tC | 2 | 0.2279 | 12.2 | 0.981 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)