| hZIP13 |
| ID: | 1485464998 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 371 (302) | ||
| Sequences: | 770 (476.7) | ||
| Seq/Len: | 2.550 | ||
| Nf(neff/√len): | 27.4 |
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: 2.550).
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 |
| 154_W | 319_W | 2.407 | 1.00 |
| 108_Q | 355_L | 2.141 | 1.00 |
| 71_S | 237_A | 2.011 | 0.99 |
| 122_F | 329_L | 1.983 | 0.99 |
| 69_I | 73_L | 1.802 | 0.99 |
| 238_A | 264_G | 1.762 | 0.98 |
| 119_G | 365_L | 1.760 | 0.98 |
| 151_L | 322_P | 1.757 | 0.98 |
| 69_I | 72_L | 1.664 | 0.97 |
| 232_H | 290_G | 1.660 | 0.97 |
| 312_A | 316_T | 1.599 | 0.96 |
| 305_G | 325_S | 1.509 | 0.94 |
| 124_H | 257_H | 1.509 | 0.94 |
| 107_K | 352_Q | 1.477 | 0.93 |
| 110_L | 235_A | 1.431 | 0.92 |
| 350_L | 354_L | 1.415 | 0.91 |
| 164_A | 350_L | 1.401 | 0.91 |
| 296_F | 300_T | 1.399 | 0.91 |
| 225_N | 232_H | 1.395 | 0.91 |
| 186_T | 361_V | 1.394 | 0.91 |
| 154_W | 323_F | 1.389 | 0.90 |
| 120_N | 250_T | 1.375 | 0.90 |
| 252_M | 296_F | 1.374 | 0.90 |
| 81_S | 165_L | 1.353 | 0.89 |
| 170_L | 177_T | 1.338 | 0.88 |
| 258_E | 261_H | 1.318 | 0.87 |
| 106_L | 259_I | 1.317 | 0.87 |
| 225_N | 352_Q | 1.290 | 0.85 |
| 262_E | 328_F | 1.285 | 0.85 |
| 89_I | 106_L | 1.280 | 0.85 |
| 247_G | 335_N | 1.277 | 0.85 |
| 118_L | 332_A | 1.273 | 0.84 |
| 258_E | 262_E | 1.270 | 0.84 |
| 250_T | 261_H | 1.269 | 0.84 |
| 70_C | 74_G | 1.265 | 0.84 |
| 324_T | 352_Q | 1.260 | 0.84 |
| 258_E | 328_F | 1.252 | 0.83 |
| 186_T | 189_A | 1.251 | 0.83 |
| 292_L | 296_F | 1.247 | 0.83 |
| 125_L | 263_V | 1.243 | 0.82 |
| 218_G | 282_L | 1.237 | 0.82 |
| 232_H | 258_E | 1.231 | 0.82 |
| 108_Q | 302_S | 1.229 | 0.82 |
| 129_A | 322_P | 1.225 | 0.81 |
| 258_E | 265_D | 1.210 | 0.80 |
| 114_L | 125_L | 1.208 | 0.80 |
| 236_V | 325_S | 1.201 | 0.79 |
| 261_H | 328_F | 1.200 | 0.79 |
| 89_I | 159_I | 1.196 | 0.79 |
| 225_N | 261_H | 1.193 | 0.79 |
| 126_L | 155_V | 1.188 | 0.78 |
| 260_P | 266_F | 1.188 | 0.78 |
| 94_G | 347_W | 1.185 | 0.78 |
| 75_S | 232_H | 1.184 | 0.78 |
| 125_L | 212_R | 1.183 | 0.78 |
| 110_L | 250_T | 1.183 | 0.78 |
| 311_P | 320_V | 1.182 | 0.78 |
| 160_L | 353_L | 1.179 | 0.78 |
| 70_C | 251_T | 1.176 | 0.77 |
| 76_L | 291_L | 1.175 | 0.77 |
| 196_H | 203_A | 1.175 | 0.77 |
| 229_N | 258_E | 1.173 | 0.77 |
| 284_L | 296_F | 1.171 | 0.77 |
| 183_K | 276_R | 1.169 | 0.77 |
| 281_K | 285_S | 1.165 | 0.76 |
| 267_A | 331_I | 1.165 | 0.76 |
| 169_F | 234_L | 1.161 | 0.76 |
| 117_L | 294_A | 1.161 | 0.76 |
| 179_Q | 183_K | 1.159 | 0.76 |
| 183_K | 354_L | 1.158 | 0.76 |
| 154_W | 352_Q | 1.153 | 0.75 |
| 68_W | 253_A | 1.146 | 0.75 |
| 218_G | 235_A | 1.144 | 0.75 |
| 94_G | 201_P | 1.141 | 0.74 |
| 125_L | 254_I | 1.139 | 0.74 |
| 186_T | 192_L | 1.136 | 0.74 |
| 288_L | 366_F | 1.133 | 0.74 |
| 274_F | 282_L | 1.131 | 0.73 |
| 225_N | 258_E | 1.117 | 0.72 |
| 181_P | 184_D | 1.115 | 0.72 |
| 90_P | 273_G | 1.113 | 0.72 |
| 153_L | 157_A | 1.110 | 0.71 |
| 282_L | 289_G | 1.110 | 0.71 |
| 79_G | 124_H | 1.108 | 0.71 |
| 73_L | 77_M | 1.103 | 0.71 |
| 232_H | 265_D | 1.098 | 0.70 |
| 275_D | 288_L | 1.097 | 0.70 |
| 157_A | 209_A | 1.096 | 0.70 |
| 75_S | 290_G | 1.096 | 0.70 |
| 246_I | 249_L | 1.094 | 0.70 |
| 117_L | 235_A | 1.091 | 0.70 |
| 295_G | 299_C | 1.089 | 0.69 |
| 132_Y | 337_L | 1.088 | 0.69 |
| 117_L | 232_H | 1.086 | 0.69 |
| 326_G | 359_G | 1.085 | 0.69 |
| 265_D | 328_F | 1.085 | 0.69 |
| 261_H | 265_D | 1.084 | 0.69 |
| 311_P | 325_S | 1.084 | 0.69 |
| 117_L | 220_L | 1.083 | 0.69 |
| 73_L | 151_L | 1.083 | 0.69 |
| 321_L | 327_G | 1.082 | 0.69 |
| 304_K | 310_S | 1.081 | 0.69 |
| 79_G | 130_W | 1.080 | 0.68 |
| 113_A | 272_A | 1.079 | 0.68 |
| 113_A | 247_G | 1.075 | 0.68 |
| 222_L | 282_L | 1.072 | 0.68 |
| 229_N | 265_D | 1.071 | 0.67 |
| 180_A | 184_D | 1.070 | 0.67 |
| 196_H | 293_G | 1.061 | 0.66 |
| 132_Y | 139_G | 1.060 | 0.66 |
| 252_M | 350_L | 1.059 | 0.66 |
| 152_G | 269_L | 1.059 | 0.66 |
| 75_S | 157_A | 1.058 | 0.66 |
| 123_L | 322_P | 1.058 | 0.66 |
| 88_V | 215_K | 1.058 | 0.66 |
| 125_L | 270_L | 1.057 | 0.66 |
| 161_T | 354_L | 1.056 | 0.66 |
| 184_D | 199_A | 1.055 | 0.66 |
| 110_L | 286_T | 1.053 | 0.66 |
| 365_L | 369_F | 1.052 | 0.65 |
| 128_E | 148_Q | 1.052 | 0.65 |
| 178_S | 193_N | 1.051 | 0.65 |
| 159_I | 333_L | 1.044 | 0.65 |
| 88_V | 202_A | 1.044 | 0.65 |
| 224_A | 336_V | 1.043 | 0.64 |
| 176_G | 183_K | 1.042 | 0.64 |
| 127_P | 152_G | 1.042 | 0.64 |
| 77_M | 357_C | 1.042 | 0.64 |
| 92_E | 99_S | 1.041 | 0.64 |
| 188_A | 191_A | 1.041 | 0.64 |
| 314_E | 333_L | 1.041 | 0.64 |
| 262_E | 291_L | 1.037 | 0.64 |
| 262_E | 266_F | 1.037 | 0.64 |
| 128_E | 131_A | 1.034 | 0.63 |
| 86_L | 318_A | 1.034 | 0.63 |
| 178_S | 181_P | 1.030 | 0.63 |
| 80_L | 129_A | 1.029 | 0.63 |
| 186_T | 191_A | 1.028 | 0.63 |
| 222_L | 328_F | 1.025 | 0.62 |
| 149_Q | 230_F | 1.025 | 0.62 |
| 90_P | 332_A | 1.024 | 0.62 |
| 232_H | 261_H | 1.023 | 0.62 |
| 106_L | 170_L | 1.023 | 0.62 |
| 84_F | 108_Q | 1.022 | 0.62 |
| 141_E | 341_L | 1.020 | 0.62 |
| 237_A | 331_I | 1.017 | 0.62 |
| 151_L | 220_L | 1.015 | 0.61 |
| 222_L | 262_E | 1.012 | 0.61 |
| 190_A | 288_L | 1.012 | 0.61 |
| 205_P | 307_V | 1.011 | 0.61 |
| 191_A | 199_A | 1.010 | 0.61 |
| 234_L | 339_D | 1.010 | 0.61 |
| 141_E | 342_E | 1.010 | 0.61 |
| 182_N | 202_A | 1.008 | 0.61 |
| 89_I | 209_A | 1.008 | 0.61 |
| 326_G | 363_M | 1.007 | 0.60 |
| 348_R | 367_S | 1.007 | 0.60 |
| 121_V | 286_T | 1.004 | 0.60 |
| 363_M | 367_S | 1.003 | 0.60 |
| 114_L | 241_L | 1.002 | 0.60 |
| 253_A | 289_G | 1.001 | 0.60 |
| 224_A | 256_L | 1.000 | 0.60 |
| 163_L | 264_G | 1.000 | 0.60 |
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
- See coupling matrix (for protein design or mutagenesis)
- 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 | |
| 4g1uA | 2 | 0.3369 | 62.8 | 0.961 | Contact Map |
| 4tkrA | 2 | 0.345 | 33 | 0.967 | Contact Map |
| 4zw9A | 1 | 0 | 28.2 | 0.968 | Contact Map |
| 3llqA | 2 | 0.345 | 25.8 | 0.969 | Contact Map |
| 4j05A | 2 | 0.3908 | 20.7 | 0.97 | Contact Map |
| 3rlbA | 2 | 0.3315 | 17.3 | 0.971 | Contact Map |
| 3h90A | 4 | 0.2453 | 14.6 | 0.972 | Contact Map |
| 4ryoA | 1 | 0 | 10.9 | 0.974 | Contact Map |
| 3o7qA | 1 | 0.3827 | 10.4 | 0.974 | Contact Map |
| 4u4vA | 1 | 0 | 9.2 | 0.975 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)