| Pr_Pfr_PHY_2 |
| ID: | 1510664255 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 500 (486) | ||
| Sequences: | 1352 (889.2) | ||
| Seq/Len: | 2.782 | ||
| Nf(neff/√len): | 40.3 |
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: 2.782).
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 |
| 153_T | 167_I | 4.704 | 1.00 |
| 157_Q | 182_S | 3.633 | 1.00 |
| 358_D | 439_V | 3.067 | 1.00 |
| 446_T | 472_A | 2.918 | 1.00 |
| 171_D | 175_N | 2.917 | 1.00 |
| 361_G | 437_F | 2.916 | 1.00 |
| 216_I | 248_V | 2.718 | 1.00 |
| 15_A | 18_D | 2.568 | 1.00 |
| 49_A | 225_P | 2.560 | 1.00 |
| 208_Y | 266_S | 2.557 | 1.00 |
| 228_M | 232_P | 2.463 | 1.00 |
| 376_D | 379_T | 2.457 | 1.00 |
| 267_I | 301_V | 2.453 | 1.00 |
| 419_L | 435_L | 2.371 | 1.00 |
| 256_L | 261_V | 2.368 | 1.00 |
| 38_E | 41_T | 2.358 | 1.00 |
| 256_L | 280_A | 2.345 | 1.00 |
| 254_Q | 463_M | 2.299 | 1.00 |
| 370_T | 380_I | 2.266 | 1.00 |
| 400_H | 480_K | 2.219 | 1.00 |
| 228_M | 235_T | 2.216 | 1.00 |
| 152_L | 304_A | 2.200 | 1.00 |
| 149_I | 179_I | 2.198 | 1.00 |
| 36_I | 238_V | 2.165 | 1.00 |
| 485_R | 488_Q | 2.162 | 1.00 |
| 30_P | 221_A | 2.151 | 1.00 |
| 209_S | 270_F | 2.110 | 1.00 |
| 20_E | 249_S | 2.093 | 1.00 |
| 240_L | 243_G | 2.041 | 1.00 |
| 409_L | 412_D | 1.956 | 0.99 |
| 206_A | 209_S | 1.934 | 0.99 |
| 359_G | 375_P | 1.930 | 0.99 |
| 253_M | 257_R | 1.854 | 0.99 |
| 193_H | 445_R | 1.845 | 0.99 |
| 17_C | 20_E | 1.842 | 0.99 |
| 466_P | 469_S | 1.782 | 0.99 |
| 30_P | 223_P | 1.778 | 0.99 |
| 146_N | 150_N | 1.774 | 0.99 |
| 144_T | 147_D | 1.756 | 0.99 |
| 221_A | 247_A | 1.752 | 0.98 |
| 220_N | 257_R | 1.736 | 0.98 |
| 104_F | 117_V | 1.735 | 0.98 |
| 118_E | 294_R | 1.729 | 0.98 |
| 166_M | 280_A | 1.705 | 0.98 |
| 466_P | 470_F | 1.669 | 0.98 |
| 352_C | 357_C | 1.652 | 0.98 |
| 258_N | 469_S | 1.619 | 0.97 |
| 187_F | 284_T | 1.610 | 0.97 |
| 71_A | 75_S | 1.588 | 0.97 |
| 44_I | 62_I | 1.572 | 0.96 |
| 362_Y | 434_L | 1.556 | 0.96 |
| 28_I | 224_Q | 1.554 | 0.96 |
| 420_L | 492_A | 1.545 | 0.96 |
| 22_I | 203_Q | 1.545 | 0.96 |
| 254_Q | 468_K | 1.542 | 0.96 |
| 47_A | 51_S | 1.532 | 0.96 |
| 46_Y | 228_M | 1.527 | 0.96 |
| 228_M | 234_N | 1.514 | 0.95 |
| 304_A | 308_L | 1.513 | 0.95 |
| 361_G | 380_I | 1.507 | 0.95 |
| 208_Y | 268_G | 1.507 | 0.95 |
| 157_Q | 184_R | 1.504 | 0.95 |
| 15_A | 19_Q | 1.498 | 0.95 |
| 370_T | 374_T | 1.491 | 0.95 |
| 203_Q | 208_Y | 1.489 | 0.95 |
| 467_R | 470_F | 1.489 | 0.95 |
| 417_A | 439_V | 1.484 | 0.95 |
| 177_R | 194_H | 1.475 | 0.94 |
| 449_G | 470_F | 1.474 | 0.94 |
| 231_K | 234_N | 1.474 | 0.94 |
| 359_G | 374_T | 1.459 | 0.94 |
| 33_A | 54_Y | 1.455 | 0.94 |
| 173_E | 194_H | 1.435 | 0.93 |
| 258_N | 467_R | 1.432 | 0.93 |
| 203_Q | 249_S | 1.411 | 0.92 |
| 359_G | 437_F | 1.411 | 0.92 |
| 216_I | 259_F | 1.407 | 0.92 |
| 46_Y | 232_P | 1.405 | 0.92 |
| 228_M | 231_K | 1.399 | 0.92 |
| 155_L | 158_E | 1.399 | 0.92 |
| 203_Q | 268_G | 1.385 | 0.92 |
| 375_P | 437_F | 1.381 | 0.91 |
| 32_G | 245_L | 1.370 | 0.91 |
| 27_A | 247_A | 1.368 | 0.91 |
| 36_I | 46_Y | 1.360 | 0.91 |
| 219_V | 256_L | 1.354 | 0.90 |
| 176_G | 469_S | 1.338 | 0.90 |
| 17_C | 251_L | 1.330 | 0.89 |
| 218_D | 262_S | 1.328 | 0.89 |
| 171_D | 174_W | 1.326 | 0.89 |
| 51_S | 62_I | 1.319 | 0.89 |
| 223_P | 247_A | 1.318 | 0.89 |
| 258_N | 466_P | 1.313 | 0.88 |
| 209_S | 274_E | 1.310 | 0.88 |
| 22_I | 204_A | 1.308 | 0.88 |
| 271_N | 312_H | 1.302 | 0.88 |
| 20_E | 250_P | 1.297 | 0.88 |
| 20_E | 203_Q | 1.297 | 0.88 |
| 403_K | 479_G | 1.296 | 0.88 |
| 21_P | 203_Q | 1.294 | 0.87 |
| 402_L | 409_L | 1.292 | 0.87 |
| 446_T | 474_Q | 1.290 | 0.87 |
| 261_V | 280_A | 1.275 | 0.86 |
| 199_D | 255_Y | 1.263 | 0.86 |
| 50_N | 224_Q | 1.261 | 0.86 |
| 33_A | 51_S | 1.258 | 0.85 |
| 150_N | 154_R | 1.252 | 0.85 |
| 37_V | 115_I | 1.252 | 0.85 |
| 25_P | 203_Q | 1.251 | 0.85 |
| 205_R | 275_L | 1.251 | 0.85 |
| 49_A | 224_Q | 1.247 | 0.85 |
| 220_N | 262_S | 1.245 | 0.85 |
| 160_S | 165_V | 1.244 | 0.84 |
| 206_A | 210_I | 1.244 | 0.84 |
| 419_L | 475_D | 1.242 | 0.84 |
| 208_Y | 248_V | 1.241 | 0.84 |
| 24_I | 203_Q | 1.237 | 0.84 |
| 174_W | 274_E | 1.236 | 0.84 |
| 129_E | 299_R | 1.236 | 0.84 |
| 425_K | 433_Y | 1.229 | 0.83 |
| 149_I | 167_I | 1.227 | 0.83 |
| 187_F | 195_F | 1.223 | 0.83 |
| 208_Y | 250_P | 1.214 | 0.82 |
| 412_D | 417_A | 1.209 | 0.82 |
| 156_I | 267_I | 1.208 | 0.82 |
| 166_M | 261_V | 1.204 | 0.82 |
| 425_K | 432_S | 1.203 | 0.82 |
| 12_K | 16_A | 1.196 | 0.81 |
| 17_C | 22_I | 1.192 | 0.81 |
| 250_P | 268_G | 1.192 | 0.81 |
| 232_P | 235_T | 1.190 | 0.81 |
| 409_L | 416_F | 1.190 | 0.81 |
| 166_M | 256_L | 1.186 | 0.80 |
| 356_R | 488_Q | 1.186 | 0.80 |
| 210_I | 242_S | 1.186 | 0.80 |
| 145_H | 308_L | 1.185 | 0.80 |
| 361_G | 435_L | 1.180 | 0.80 |
| 162_Y | 265_T | 1.179 | 0.80 |
| 85_L | 435_L | 1.173 | 0.79 |
| 47_A | 59_D | 1.172 | 0.79 |
| 21_P | 24_I | 1.171 | 0.79 |
| 360_I | 371_Y | 1.168 | 0.79 |
| 34_M | 116_E | 1.165 | 0.79 |
| 176_G | 258_N | 1.165 | 0.79 |
| 401_M | 480_K | 1.165 | 0.79 |
| 258_N | 470_F | 1.164 | 0.79 |
| 380_I | 437_F | 1.162 | 0.78 |
| 110_E | 236_E | 1.160 | 0.78 |
| 252_H | 264_S | 1.156 | 0.78 |
| 45_V | 112_Y | 1.154 | 0.78 |
| 156_I | 279_V | 1.154 | 0.78 |
| 46_Y | 231_K | 1.153 | 0.78 |
| 22_I | 207_M | 1.152 | 0.78 |
| 199_D | 258_N | 1.149 | 0.77 |
| 33_A | 117_V | 1.149 | 0.77 |
| 39_K | 113_Y | 1.149 | 0.77 |
| 230_H | 235_T | 1.148 | 0.77 |
| 166_M | 259_F | 1.146 | 0.77 |
| 208_Y | 251_L | 1.143 | 0.77 |
| 219_V | 262_S | 1.141 | 0.77 |
| 24_I | 237_A | 1.139 | 0.77 |
| 200_I | 204_A | 1.139 | 0.77 |
| 175_N | 194_H | 1.139 | 0.77 |
| 266_S | 280_A | 1.138 | 0.76 |
| 30_P | 222_E | 1.135 | 0.76 |
| 199_D | 246_R | 1.134 | 0.76 |
| 109_H | 114_I | 1.132 | 0.76 |
| 51_S | 59_D | 1.130 | 0.76 |
| 212_P | 270_F | 1.126 | 0.75 |
| 361_G | 375_P | 1.126 | 0.75 |
| 241_S | 248_V | 1.123 | 0.75 |
| 169_Q | 177_R | 1.116 | 0.74 |
| 140_R | 302_E | 1.116 | 0.74 |
| 26_N | 249_S | 1.112 | 0.74 |
| 44_I | 47_A | 1.111 | 0.74 |
| 154_R | 182_S | 1.109 | 0.74 |
| 37_V | 42_Q | 1.101 | 0.73 |
| 153_T | 281_C | 1.101 | 0.73 |
| 319_Y | 323_V | 1.100 | 0.73 |
| 205_R | 467_R | 1.097 | 0.73 |
| 168_Y | 176_G | 1.096 | 0.73 |
| 162_Y | 266_S | 1.095 | 0.72 |
| 307_R | 310_L | 1.093 | 0.72 |
| 36_I | 112_Y | 1.093 | 0.72 |
| 177_R | 192_N | 1.091 | 0.72 |
| 377_Q | 381_N | 1.085 | 0.71 |
| 105_L | 291_R | 1.082 | 0.71 |
| 168_Y | 258_N | 1.082 | 0.71 |
| 398_H | 405_D | 1.081 | 0.71 |
| 18_D | 202_A | 1.080 | 0.71 |
| 199_D | 470_F | 1.079 | 0.71 |
| 72_N | 75_S | 1.074 | 0.70 |
| 401_M | 404_E | 1.072 | 0.70 |
| 219_V | 257_R | 1.069 | 0.70 |
| 21_P | 25_P | 1.062 | 0.69 |
| 16_A | 19_Q | 1.062 | 0.69 |
| 449_G | 466_P | 1.062 | 0.69 |
| 29_Q | 32_G | 1.062 | 0.69 |
| 199_D | 469_S | 1.058 | 0.69 |
| 199_D | 252_H | 1.058 | 0.69 |
| 16_A | 251_L | 1.057 | 0.69 |
| 188_T | 471_E | 1.057 | 0.69 |
| 443_E | 488_Q | 1.056 | 0.69 |
| 171_D | 177_R | 1.054 | 0.68 |
| 189_S | 195_F | 1.053 | 0.68 |
| 37_V | 44_I | 1.050 | 0.68 |
| 168_Y | 469_S | 1.049 | 0.68 |
| 35_L | 51_S | 1.048 | 0.68 |
| 263_A | 283_H | 1.046 | 0.67 |
| 22_I | 268_G | 1.044 | 0.67 |
| 20_E | 453_K | 1.043 | 0.67 |
| 449_G | 469_S | 1.041 | 0.67 |
| 387_L | 419_L | 1.040 | 0.67 |
| 255_Y | 258_N | 1.039 | 0.67 |
| 352_C | 371_Y | 1.038 | 0.67 |
| 176_G | 199_D | 1.037 | 0.66 |
| 247_A | 250_P | 1.037 | 0.66 |
| 450_K | 454_L | 1.035 | 0.66 |
| 374_T | 437_F | 1.034 | 0.66 |
| 133_Q | 139_L | 1.031 | 0.66 |
| 211_N | 266_S | 1.028 | 0.65 |
| 162_Y | 217_P | 1.028 | 0.65 |
| 205_R | 246_R | 1.028 | 0.65 |
| 413_G | 416_F | 1.026 | 0.65 |
| 17_C | 203_Q | 1.026 | 0.65 |
| 406_A | 409_L | 1.026 | 0.65 |
| 252_H | 268_G | 1.025 | 0.65 |
| 17_C | 21_P | 1.024 | 0.65 |
| 13_L | 16_A | 1.021 | 0.65 |
| 39_K | 108_R | 1.021 | 0.65 |
| 116_E | 239_N | 1.018 | 0.64 |
| 199_D | 205_R | 1.017 | 0.64 |
| 145_H | 351_W | 1.013 | 0.64 |
| 17_C | 204_A | 1.009 | 0.63 |
| 168_Y | 199_D | 1.006 | 0.63 |
| 447_W | 470_F | 1.006 | 0.63 |
| 269_I | 301_V | 1.004 | 0.63 |
| 230_H | 234_N | 1.002 | 0.63 |
| 203_Q | 250_P | 1.001 | 0.62 |
| 387_L | 421_A | 1.001 | 0.62 |
| 406_A | 412_D | 1.001 | 0.62 |
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 | |
| 4ourA | 1 | 0.848 | 100 | 0.199 | Contact Map |
| 4q0jA | 1 | 0.942 | 100 | 0.275 | Contact Map |
| 3zq5A | 1 | 0.972 | 100 | 0.288 | Contact Map |
| 3nhqA | 8 | 0.934 | 100 | 0.313 | Contact Map |
| 4gw9A | 4 | 0.964 | 100 | 0.36 | Contact Map |
| 4r70A | 2 | 0 | 100 | 0.384 | Contact Map |
| 4s21A | 2 | 0 | 100 | 0.398 | Contact Map |
| 4cqhA | 1 | 0.586 | 100 | 0.534 | Contact Map |
| 2oolA | 2 | 0.59 | 100 | 0.56 | Contact Map |
| 4bwiA | 2 | 0.72 | 100 | 0.599 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)