| M Janaschii PGM |
| ID: | 1491414691 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 411 (365) | ||
| Sequences: | 715 (540.2) | ||
| Seq/Len: | 1.959 | ||
| Nf(neff/√len): | 28.3 |
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: 1.959).
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 |
| 27_K | 378_N | 4.026 | 1.00 |
| 27_K | 380_F | 3.931 | 1.00 |
| 37_I | 363_V | 3.528 | 1.00 |
| 310_G | 353_K | 3.224 | 1.00 |
| 16_D | 25_P | 2.996 | 1.00 |
| 213_R | 219_P | 2.797 | 1.00 |
| 278_N | 281_G | 2.728 | 1.00 |
| 211_E | 215_K | 2.725 | 1.00 |
| 72_V | 235_E | 2.511 | 1.00 |
| 280_M | 325_M | 2.507 | 1.00 |
| 311_N | 314_L | 2.445 | 1.00 |
| 264_D | 293_Y | 2.395 | 1.00 |
| 43_C | 382_C | 2.384 | 1.00 |
| 88_L | 151_V | 2.375 | 1.00 |
| 31_T | 35_D | 2.366 | 1.00 |
| 378_N | 381_A | 2.300 | 1.00 |
| 238_S | 244_K | 2.277 | 1.00 |
| 245_G | 263_L | 2.269 | 1.00 |
| 284_K | 288_E | 2.210 | 1.00 |
| 307_S | 349_P | 2.204 | 1.00 |
| 127_E | 202_K | 2.171 | 0.99 |
| 246_A | 293_Y | 2.139 | 0.99 |
| 247_C | 258_A | 2.119 | 0.99 |
| 88_L | 94_A | 2.076 | 0.99 |
| 36_K | 40_E | 2.039 | 0.99 |
| 269_E | 278_N | 2.021 | 0.99 |
| 41_G | 363_V | 1.962 | 0.99 |
| 17_R | 358_D | 1.956 | 0.99 |
| 339_Y | 366_G | 1.944 | 0.99 |
| 17_R | 351_E | 1.889 | 0.98 |
| 247_C | 254_I | 1.863 | 0.98 |
| 246_A | 289_A | 1.826 | 0.98 |
| 89_K | 153_R | 1.803 | 0.97 |
| 31_T | 34_M | 1.791 | 0.97 |
| 127_E | 206_H | 1.776 | 0.97 |
| 210_E | 213_R | 1.774 | 0.97 |
| 140_F | 150_L | 1.774 | 0.97 |
| 31_T | 319_L | 1.768 | 0.97 |
| 7_V | 298_V | 1.762 | 0.97 |
| 34_M | 342_L | 1.758 | 0.97 |
| 158_S | 185_A | 1.729 | 0.96 |
| 124_L | 220_A | 1.700 | 0.96 |
| 11_I | 14_L | 1.694 | 0.96 |
| 140_F | 195_L | 1.666 | 0.95 |
| 10_I | 64_I | 1.666 | 0.95 |
| 28_E | 316_K | 1.662 | 0.95 |
| 342_L | 363_V | 1.639 | 0.95 |
| 68_N | 71_E | 1.617 | 0.94 |
| 100_A | 108_V | 1.598 | 0.94 |
| 139_I | 153_R | 1.598 | 0.94 |
| 211_E | 214_K | 1.594 | 0.94 |
| 15_G | 347_S | 1.582 | 0.93 |
| 92_D | 153_R | 1.579 | 0.93 |
| 47_N | 51_I | 1.554 | 0.93 |
| 211_E | 217_L | 1.553 | 0.93 |
| 199_V | 222_I | 1.536 | 0.92 |
| 194_K | 198_I | 1.534 | 0.92 |
| 277_T | 282_K | 1.530 | 0.92 |
| 352_M | 356_S | 1.512 | 0.91 |
| 82_F | 260_M | 1.493 | 0.91 |
| 250_G | 282_K | 1.484 | 0.90 |
| 198_I | 201_E | 1.482 | 0.90 |
| 138_V | 150_L | 1.467 | 0.89 |
| 18_P | 22_G | 1.463 | 0.89 |
| 11_I | 322_I | 1.436 | 0.88 |
| 196_L | 225_P | 1.427 | 0.88 |
| 103_D | 109_L | 1.425 | 0.88 |
| 113_A | 116_I | 1.404 | 0.87 |
| 40_E | 365_W | 1.403 | 0.87 |
| 140_F | 223_I | 1.364 | 0.84 |
| 64_I | 343_T | 1.363 | 0.84 |
| 268_V | 285_A | 1.359 | 0.84 |
| 366_G | 369_V | 1.346 | 0.83 |
| 312_Y | 316_K | 1.342 | 0.83 |
| 197_K | 200_Y | 1.334 | 0.83 |
| 306_A | 314_L | 1.327 | 0.82 |
| 266_I | 289_A | 1.301 | 0.80 |
| 207_P | 216_G | 1.295 | 0.80 |
| 283_A | 298_V | 1.295 | 0.80 |
| 287_V | 328_Y | 1.283 | 0.79 |
| 235_E | 239_E | 1.282 | 0.79 |
| 124_L | 206_H | 1.277 | 0.79 |
| 272_T | 277_T | 1.269 | 0.78 |
| 97_C | 148_G | 1.251 | 0.77 |
| 209_N | 212_R | 1.242 | 0.76 |
| 102_V | 222_I | 1.240 | 0.76 |
| 123_E | 208_I | 1.240 | 0.76 |
| 288_E | 291_K | 1.235 | 0.75 |
| 181_D | 186_K | 1.235 | 0.75 |
| 58_D | 73_Y | 1.224 | 0.74 |
| 235_E | 240_K | 1.215 | 0.74 |
| 10_I | 297_L | 1.214 | 0.73 |
| 9_F | 322_I | 1.213 | 0.73 |
| 345_D | 355_H | 1.213 | 0.73 |
| 15_G | 343_T | 1.209 | 0.73 |
| 120_E | 208_I | 1.201 | 0.72 |
| 42_I | 362_I | 1.197 | 0.72 |
| 100_A | 224_L | 1.195 | 0.72 |
| 117_S | 120_E | 1.183 | 0.71 |
| 237_F | 243_M | 1.175 | 0.70 |
| 63_A | 102_V | 1.172 | 0.70 |
| 246_A | 296_V | 1.169 | 0.69 |
| 76_R | 355_H | 1.155 | 0.68 |
| 282_K | 302_G | 1.154 | 0.68 |
| 273_G | 277_T | 1.152 | 0.68 |
| 346_H | 355_H | 1.151 | 0.68 |
| 58_D | 78_P | 1.148 | 0.67 |
| 129_D | 139_I | 1.145 | 0.67 |
| 9_F | 95_F | 1.142 | 0.67 |
| 329_V | 338_V | 1.140 | 0.67 |
| 206_H | 209_N | 1.138 | 0.66 |
| 237_F | 245_G | 1.137 | 0.66 |
| 5_K | 294_D | 1.137 | 0.66 |
| 39_K | 375_T | 1.136 | 0.66 |
| 251_T | 254_I | 1.134 | 0.66 |
| 212_R | 217_L | 1.134 | 0.66 |
| 74_T | 78_P | 1.131 | 0.66 |
| 9_F | 300_V | 1.125 | 0.65 |
| 303_A | 318_V | 1.123 | 0.65 |
| 308_H | 345_D | 1.119 | 0.64 |
| 146_Y | 224_L | 1.115 | 0.64 |
| 316_K | 320_E | 1.113 | 0.64 |
| 56_G | 227_G | 1.112 | 0.64 |
| 205_N | 210_E | 1.112 | 0.64 |
| 27_K | 381_A | 1.103 | 0.63 |
| 14_L | 344_G | 1.100 | 0.63 |
| 41_G | 365_W | 1.095 | 0.62 |
| 112_R | 115_R | 1.095 | 0.62 |
| 236_K | 239_E | 1.095 | 0.62 |
| 160_R | 180_D | 1.092 | 0.62 |
| 62_L | 67_Y | 1.089 | 0.61 |
| 308_H | 355_H | 1.088 | 0.61 |
| 349_P | 356_S | 1.083 | 0.61 |
| 138_V | 152_L | 1.082 | 0.61 |
| 15_G | 64_I | 1.081 | 0.61 |
| 122_E | 126_K | 1.074 | 0.60 |
| 52_G | 357_A | 1.073 | 0.60 |
| 348_T | 355_H | 1.071 | 0.59 |
| 138_V | 191_I | 1.068 | 0.59 |
| 146_Y | 226_R | 1.065 | 0.59 |
| 23_L | 28_E | 1.064 | 0.59 |
| 122_E | 142_S | 1.063 | 0.59 |
| 255_K | 267_E | 1.057 | 0.58 |
| 98_N | 147_R | 1.049 | 0.57 |
| 207_P | 217_L | 1.049 | 0.57 |
| 77_G | 225_P | 1.048 | 0.57 |
| 23_L | 317_E | 1.046 | 0.57 |
| 115_R | 309_D | 1.044 | 0.57 |
| 304_D | 308_H | 1.034 | 0.55 |
| 108_V | 111_R | 1.032 | 0.55 |
| 244_K | 293_Y | 1.031 | 0.55 |
| 269_E | 285_A | 1.030 | 0.55 |
| 376_E | 381_A | 1.029 | 0.55 |
| 60_A | 299_N | 1.028 | 0.55 |
| 14_L | 319_L | 1.026 | 0.55 |
| 249_C | 258_A | 1.021 | 0.54 |
| 123_E | 126_K | 1.019 | 0.54 |
| 304_D | 345_D | 1.016 | 0.53 |
| 206_H | 212_R | 1.011 | 0.53 |
| 78_P | 110_D | 1.010 | 0.53 |
| 269_E | 281_G | 1.009 | 0.53 |
| 304_D | 355_H | 1.009 | 0.53 |
| 272_T | 276_K | 1.004 | 0.52 |
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 | |
| 3kd8A | 2 | 0.8954 | 100 | 0.279 | Contact Map |
| 2zktA | 2 | 0.9343 | 100 | 0.3 | Contact Map |
| 1o98A | 1 | 0.9002 | 99.8 | 0.853 | Contact Map |
| 4my4A | 1 | 0.8954 | 99.8 | 0.86 | Contact Map |
| 3igzB | 1 | 0.8856 | 99.7 | 0.871 | Contact Map |
| 1zedA | 1 | 0.8224 | 99.6 | 0.885 | Contact Map |
| 3tg0A | 4 | 0.7786 | 99.6 | 0.888 | Contact Map |
| 1k7hA | 2 | 0.8127 | 99.4 | 0.896 | Contact Map |
| 3m7vA | 2 | 0.8054 | 99.3 | 0.903 | Contact Map |
| 3a52A | 2 | 0.7251 | 99.2 | 0.907 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)