| DrBphP_4O01 |
| ID: | 1489517212 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 480 (471) | ||
| Sequences: | 1335 (874.3) | ||
| Seq/Len: | 2.834 | ||
| 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: 2.834).
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 |
| 149_T | 163_L | 4.780 | 1.00 |
| 153_R | 178_A | 3.606 | 1.00 |
| 354_G | 431_P | 2.910 | 1.00 |
| 167_A | 171_T | 2.870 | 1.00 |
| 357_I | 429_L | 2.825 | 1.00 |
| 212_T | 244_T | 2.693 | 1.00 |
| 204_Y | 262_S | 2.604 | 1.00 |
| 17_E | 20_E | 2.581 | 1.00 |
| 372_P | 375_A | 2.572 | 1.00 |
| 224_P | 228_P | 2.498 | 1.00 |
| 252_L | 257_V | 2.493 | 1.00 |
| 51_L | 221_P | 2.488 | 1.00 |
| 263_V | 297_G | 2.460 | 1.00 |
| 413_L | 427_V | 2.446 | 1.00 |
| 250_Q | 439_D | 2.443 | 1.00 |
| 252_L | 276_A | 2.334 | 1.00 |
| 366_T | 376_V | 2.316 | 1.00 |
| 40_D | 43_S | 2.292 | 1.00 |
| 394_D | 456_Y | 2.288 | 1.00 |
| 224_P | 231_N | 2.255 | 1.00 |
| 145_A | 175_I | 2.236 | 1.00 |
| 38_T | 234_T | 2.196 | 1.00 |
| 32_P | 217_A | 2.180 | 1.00 |
| 148_A | 300_L | 2.163 | 1.00 |
| 461_H | 464_E | 2.155 | 1.00 |
| 205_T | 266_V | 2.137 | 1.00 |
| 22_E | 245_S | 2.092 | 1.00 |
| 236_L | 239_A | 2.086 | 1.00 |
| 249_M | 253_R | 1.920 | 0.99 |
| 19_C | 22_E | 1.908 | 0.99 |
| 189_H | 437_V | 1.894 | 0.99 |
| 403_G | 406_L | 1.893 | 0.99 |
| 202_A | 205_T | 1.890 | 0.99 |
| 355_G | 371_P | 1.881 | 0.99 |
| 120_E | 290_R | 1.840 | 0.99 |
| 106_L | 119_F | 1.839 | 0.99 |
| 32_P | 219_A | 1.835 | 0.99 |
| 140_N | 143_A | 1.797 | 0.99 |
| 153_R | 180_R | 1.734 | 0.98 |
| 442_P | 445_S | 1.713 | 0.98 |
| 217_A | 243_A | 1.701 | 0.98 |
| 348_L | 353_A | 1.696 | 0.98 |
| 142_R | 146_E | 1.696 | 0.98 |
| 46_V | 64_L | 1.693 | 0.98 |
| 162_M | 276_A | 1.693 | 0.98 |
| 224_P | 230_T | 1.691 | 0.98 |
| 250_Q | 444_H | 1.654 | 0.98 |
| 254_N | 445_S | 1.646 | 0.98 |
| 414_L | 468_A | 1.632 | 0.97 |
| 183_L | 280_Q | 1.630 | 0.97 |
| 216_R | 253_R | 1.619 | 0.97 |
| 48_Q | 224_P | 1.616 | 0.97 |
| 357_I | 376_V | 1.573 | 0.97 |
| 358_L | 426_L | 1.570 | 0.97 |
| 366_T | 370_V | 1.564 | 0.96 |
| 227_N | 230_T | 1.561 | 0.96 |
| 24_I | 199_Q | 1.557 | 0.96 |
| 300_L | 304_V | 1.556 | 0.96 |
| 30_I | 220_V | 1.523 | 0.96 |
| 17_E | 21_R | 1.519 | 0.96 |
| 204_Y | 264_S | 1.519 | 0.96 |
| 442_P | 446_F | 1.518 | 0.96 |
| 224_P | 227_N | 1.507 | 0.95 |
| 67_Q | 71_A | 1.504 | 0.95 |
| 199_Q | 204_Y | 1.474 | 0.95 |
| 35_A | 56_F | 1.458 | 0.94 |
| 199_Q | 245_S | 1.452 | 0.94 |
| 19_C | 247_M | 1.441 | 0.94 |
| 49_M | 53_A | 1.432 | 0.93 |
| 48_Q | 228_P | 1.416 | 0.93 |
| 443_R | 446_F | 1.415 | 0.93 |
| 29_S | 243_A | 1.409 | 0.93 |
| 173_E | 190_R | 1.407 | 0.93 |
| 212_T | 255_M | 1.407 | 0.93 |
| 411_A | 431_P | 1.398 | 0.92 |
| 201_R | 271_L | 1.397 | 0.92 |
| 151_T | 154_E | 1.391 | 0.92 |
| 228_P | 231_N | 1.373 | 0.91 |
| 355_G | 429_L | 1.355 | 0.91 |
| 355_G | 370_V | 1.354 | 0.91 |
| 34_G | 241_L | 1.345 | 0.90 |
| 214_D | 258_G | 1.340 | 0.90 |
| 167_A | 170_A | 1.337 | 0.90 |
| 22_E | 199_Q | 1.327 | 0.89 |
| 195_D | 251_Y | 1.327 | 0.89 |
| 267_V | 308_E | 1.326 | 0.89 |
| 38_T | 48_Q | 1.326 | 0.89 |
| 254_N | 443_R | 1.321 | 0.89 |
| 169_D | 190_R | 1.318 | 0.89 |
| 23_P | 199_Q | 1.316 | 0.89 |
| 396_L | 403_G | 1.311 | 0.89 |
| 172_G | 445_S | 1.310 | 0.89 |
| 215_T | 252_L | 1.308 | 0.88 |
| 53_A | 64_L | 1.306 | 0.88 |
| 156_T | 161_V | 1.294 | 0.88 |
| 24_I | 200_A | 1.293 | 0.88 |
| 257_V | 276_A | 1.287 | 0.87 |
| 35_A | 53_A | 1.285 | 0.87 |
| 397_G | 455_G | 1.285 | 0.87 |
| 22_E | 246_P | 1.283 | 0.87 |
| 205_T | 270_Q | 1.279 | 0.87 |
| 254_N | 446_F | 1.274 | 0.87 |
| 202_A | 206_R | 1.264 | 0.86 |
| 162_M | 255_M | 1.263 | 0.86 |
| 41_G | 115_L | 1.259 | 0.86 |
| 371_P | 429_L | 1.251 | 0.85 |
| 14_I | 18_N | 1.245 | 0.85 |
| 39_A | 117_L | 1.245 | 0.85 |
| 51_L | 220_V | 1.245 | 0.85 |
| 152_V | 263_V | 1.243 | 0.85 |
| 195_D | 254_N | 1.235 | 0.84 |
| 39_A | 44_G | 1.229 | 0.84 |
| 216_R | 258_G | 1.226 | 0.84 |
| 52_N | 220_V | 1.225 | 0.84 |
| 356_L | 367_L | 1.224 | 0.84 |
| 24_I | 203_L | 1.222 | 0.83 |
| 406_L | 411_A | 1.221 | 0.83 |
| 26_I | 199_Q | 1.218 | 0.83 |
| 219_A | 243_A | 1.217 | 0.83 |
| 146_E | 150_Q | 1.213 | 0.83 |
| 141_L | 304_V | 1.210 | 0.83 |
| 204_Y | 244_T | 1.208 | 0.82 |
| 199_Q | 264_S | 1.195 | 0.82 |
| 107_T | 287_P | 1.194 | 0.81 |
| 419_G | 425_C | 1.189 | 0.81 |
| 172_G | 254_N | 1.189 | 0.81 |
| 246_P | 264_S | 1.188 | 0.81 |
| 206_R | 238_G | 1.186 | 0.81 |
| 204_Y | 246_P | 1.184 | 0.81 |
| 183_L | 191_F | 1.181 | 0.80 |
| 126_H | 295_Y | 1.178 | 0.80 |
| 419_G | 424_E | 1.177 | 0.80 |
| 111_V | 116_I | 1.175 | 0.80 |
| 35_A | 119_F | 1.173 | 0.80 |
| 248_H | 260_S | 1.172 | 0.80 |
| 19_C | 24_I | 1.171 | 0.80 |
| 357_I | 427_V | 1.170 | 0.80 |
| 47_L | 114_L | 1.161 | 0.79 |
| 20_E | 198_A | 1.159 | 0.79 |
| 184_H | 447_D | 1.158 | 0.79 |
| 145_A | 163_L | 1.157 | 0.79 |
| 204_Y | 247_M | 1.156 | 0.78 |
| 262_S | 276_A | 1.153 | 0.78 |
| 162_M | 257_V | 1.152 | 0.78 |
| 357_I | 371_P | 1.151 | 0.78 |
| 41_G | 110_R | 1.151 | 0.78 |
| 27_P | 199_Q | 1.149 | 0.78 |
| 152_V | 275_I | 1.149 | 0.78 |
| 195_D | 446_F | 1.145 | 0.78 |
| 48_Q | 227_N | 1.144 | 0.77 |
| 195_D | 242_R | 1.144 | 0.77 |
| 32_P | 218_A | 1.142 | 0.77 |
| 36_L | 118_E | 1.141 | 0.77 |
| 226_L | 231_N | 1.139 | 0.77 |
| 196_I | 200_A | 1.137 | 0.77 |
| 376_V | 429_L | 1.135 | 0.77 |
| 23_P | 26_I | 1.132 | 0.76 |
| 28_G | 245_S | 1.132 | 0.76 |
| 170_A | 270_Q | 1.129 | 0.76 |
| 254_N | 442_P | 1.129 | 0.76 |
| 158_F | 261_L | 1.128 | 0.76 |
| 18_N | 247_M | 1.123 | 0.76 |
| 171_T | 190_R | 1.122 | 0.76 |
| 162_M | 252_L | 1.118 | 0.75 |
| 237_G | 244_T | 1.117 | 0.75 |
| 195_D | 248_H | 1.112 | 0.75 |
| 19_C | 199_Q | 1.111 | 0.75 |
| 395_A | 456_Y | 1.109 | 0.74 |
| 38_T | 114_L | 1.106 | 0.74 |
| 251_Y | 254_N | 1.105 | 0.74 |
| 403_G | 410_A | 1.105 | 0.74 |
| 49_M | 61_P | 1.103 | 0.74 |
| 158_F | 262_S | 1.102 | 0.74 |
| 18_N | 21_R | 1.101 | 0.74 |
| 164_Y | 445_S | 1.097 | 0.73 |
| 53_A | 61_P | 1.097 | 0.73 |
| 149_T | 277_C | 1.095 | 0.73 |
| 215_T | 258_G | 1.094 | 0.73 |
| 46_V | 49_M | 1.094 | 0.73 |
| 165_K | 173_E | 1.091 | 0.73 |
| 173_E | 188_G | 1.090 | 0.73 |
| 195_D | 201_R | 1.089 | 0.72 |
| 31_Q | 34_G | 1.089 | 0.72 |
| 208_L | 266_V | 1.088 | 0.72 |
| 26_I | 233_P | 1.086 | 0.72 |
| 303_Q | 306_V | 1.085 | 0.72 |
| 348_L | 367_L | 1.084 | 0.72 |
| 150_Q | 178_A | 1.083 | 0.72 |
| 164_Y | 254_N | 1.079 | 0.71 |
| 167_A | 173_E | 1.079 | 0.71 |
| 195_D | 445_S | 1.074 | 0.71 |
| 164_Y | 172_G | 1.071 | 0.71 |
| 185_A | 191_F | 1.070 | 0.71 |
| 24_I | 264_S | 1.069 | 0.70 |
| 393_T | 399_L | 1.068 | 0.70 |
| 243_A | 246_P | 1.066 | 0.70 |
| 265_V | 275_I | 1.066 | 0.70 |
| 19_C | 200_A | 1.059 | 0.69 |
| 383_L | 413_L | 1.057 | 0.69 |
| 316_R | 466_E | 1.056 | 0.69 |
| 112_G | 232_A | 1.053 | 0.69 |
| 197_P | 254_N | 1.051 | 0.69 |
| 400_W | 403_G | 1.050 | 0.68 |
| 172_G | 195_D | 1.050 | 0.68 |
| 65_R | 68_T | 1.047 | 0.68 |
| 259_S | 279_H | 1.045 | 0.68 |
| 352_R | 464_E | 1.044 | 0.68 |
| 158_F | 213_A | 1.041 | 0.67 |
| 207_H | 262_S | 1.040 | 0.67 |
| 201_R | 443_R | 1.038 | 0.67 |
| 248_H | 264_S | 1.036 | 0.67 |
| 327_A | 330_A | 1.034 | 0.67 |
| 179_R | 182_G | 1.034 | 0.67 |
| 248_H | 251_Y | 1.030 | 0.66 |
| 383_L | 415_A | 1.030 | 0.66 |
| 129_R | 135_L | 1.028 | 0.66 |
| 215_T | 253_R | 1.027 | 0.66 |
| 27_P | 264_S | 1.027 | 0.66 |
| 39_A | 46_V | 1.026 | 0.66 |
| 201_R | 242_R | 1.026 | 0.66 |
| 395_A | 398_Q | 1.025 | 0.66 |
| 199_Q | 246_P | 1.023 | 0.65 |
| 375_A | 406_L | 1.023 | 0.65 |
| 136_E | 298_R | 1.022 | 0.65 |
| 330_A | 339_T | 1.021 | 0.65 |
| 198_A | 202_A | 1.019 | 0.65 |
| 373_A | 377_D | 1.019 | 0.65 |
| 226_L | 230_T | 1.019 | 0.65 |
| 419_G | 478_A | 1.016 | 0.65 |
| 353_A | 464_E | 1.015 | 0.65 |
| 252_L | 258_G | 1.015 | 0.65 |
| 407_A | 410_A | 1.014 | 0.64 |
| 251_Y | 446_F | 1.013 | 0.64 |
| 19_C | 23_P | 1.012 | 0.64 |
| 72_L | 379_L | 1.011 | 0.64 |
| 203_L | 207_H | 1.010 | 0.64 |
| 417_S | 428_W | 1.010 | 0.64 |
| 15_T | 18_N | 1.009 | 0.64 |
| 164_Y | 195_D | 1.007 | 0.64 |
| 37_L | 53_A | 1.003 | 0.63 |
| 366_T | 373_A | 1.002 | 0.63 |
| 197_P | 251_Y | 1.001 | 0.63 |
| 121_P | 282_P | 1.000 | 0.63 |
| 440_L | 443_R | 1.000 | 0.63 |
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 | |
| 4ourA | 1 | 0.8562 | 100 | 0.221 | Contact Map |
| 4q0jA | 1 | 0.9812 | 100 | 0.271 | Contact Map |
| 3zq5A | 1 | 0.9854 | 100 | 0.317 | Contact Map |
| 3nhqA | 8 | 0.9458 | 100 | 0.335 | Contact Map |
| 4gw9A | 4 | 0.9771 | 100 | 0.375 | Contact Map |
| 4r70A | 2 | 0 | 100 | 0.402 | Contact Map |
| 4s21A | 2 | 0 | 100 | 0.423 | Contact Map |
| 4cqhA | 1 | 0.6292 | 100 | 0.514 | Contact Map |
| 2oolA | 2 | 0.6083 | 100 | 0.55 | Contact Map |
| 4bwiA | 2 | 0.7292 | 100 | 0.622 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)