| Glcr |
| ID: | 1485759457 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 477 (404) | ||
| Sequences: | 412 (215.6) | ||
| Seq/Len: | 1.020 | ||
| Nf(neff/√len): | 10.7 |
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: 1.020).
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 |
| 401_C | 404_N | 3.259 | 1.00 |
| 401_C | 406_E | 3.028 | 1.00 |
| 400_Y | 404_N | 2.630 | 1.00 |
| 400_Y | 406_E | 2.563 | 0.99 |
| 402_F | 406_E | 2.191 | 0.98 |
| 324_R | 327_Q | 2.143 | 0.97 |
| 63_D | 67_C | 2.132 | 0.97 |
| 58_C | 67_C | 2.046 | 0.96 |
| 404_N | 407_V | 1.999 | 0.96 |
| 401_C | 407_V | 1.911 | 0.94 |
| 160_L | 178_A | 1.870 | 0.93 |
| 71_T | 77_A | 1.853 | 0.93 |
| 403_L | 406_E | 1.813 | 0.92 |
| 322_F | 347_L | 1.795 | 0.91 |
| 233_Y | 245_E | 1.771 | 0.90 |
| 401_C | 405_K | 1.763 | 0.90 |
| 400_Y | 403_L | 1.755 | 0.90 |
| 350_S | 385_D | 1.749 | 0.90 |
| 400_Y | 407_V | 1.728 | 0.89 |
| 58_C | 63_D | 1.721 | 0.89 |
| 60_R | 70_D | 1.664 | 0.86 |
| 58_C | 68_W | 1.611 | 0.84 |
| 286_K | 292_V | 1.611 | 0.84 |
| 183_S | 238_N | 1.583 | 0.82 |
| 169_L | 233_Y | 1.564 | 0.81 |
| 241_W | 245_E | 1.557 | 0.81 |
| 172_T | 175_A | 1.557 | 0.81 |
| 146_T | 195_D | 1.505 | 0.78 |
| 148_G | 152_S | 1.487 | 0.76 |
| 246_G | 250_H | 1.480 | 0.76 |
| 145_Y | 176_I | 1.476 | 0.76 |
| 242_L | 322_F | 1.466 | 0.75 |
| 350_S | 382_L | 1.458 | 0.74 |
| 163_L | 278_F | 1.456 | 0.74 |
| 231_M | 358_L | 1.456 | 0.74 |
| 225_R | 291_N | 1.447 | 0.74 |
| 97_F | 120_Q | 1.434 | 0.73 |
| 245_E | 271_G | 1.423 | 0.72 |
| 170_H | 174_N | 1.423 | 0.72 |
| 402_F | 407_V | 1.411 | 0.71 |
| 393_G | 406_E | 1.409 | 0.71 |
| 174_N | 282_W | 1.403 | 0.70 |
| 400_Y | 405_K | 1.401 | 0.70 |
| 187_K | 194_I | 1.376 | 0.68 |
| 192_L | 350_S | 1.376 | 0.68 |
| 245_E | 272_W | 1.368 | 0.67 |
| 66_S | 79_I | 1.367 | 0.67 |
| 173_R | 177_H | 1.357 | 0.67 |
| 393_G | 404_N | 1.350 | 0.66 |
| 322_F | 350_S | 1.349 | 0.66 |
| 245_E | 249_L | 1.343 | 0.65 |
| 322_F | 361_H | 1.333 | 0.65 |
| 347_L | 350_S | 1.323 | 0.64 |
| 172_T | 176_I | 1.321 | 0.64 |
| 319_F | 391_F | 1.316 | 0.63 |
| 171_C | 184_F | 1.315 | 0.63 |
| 69_P | 286_K | 1.304 | 0.62 |
| 240_C | 270_I | 1.300 | 0.62 |
| 163_L | 398_V | 1.296 | 0.61 |
| 148_G | 156_L | 1.290 | 0.61 |
| 47_L | 60_R | 1.289 | 0.61 |
| 67_C | 82_P | 1.285 | 0.60 |
| 238_N | 361_H | 1.283 | 0.60 |
| 168_K | 174_N | 1.281 | 0.60 |
| 410_E | 415_W | 1.276 | 0.60 |
| 224_C | 245_E | 1.271 | 0.59 |
| 233_Y | 241_W | 1.265 | 0.59 |
| 281_P | 285_V | 1.259 | 0.58 |
| 305_W | 312_F | 1.247 | 0.57 |
| 170_H | 270_I | 1.247 | 0.57 |
| 176_I | 229_V | 1.246 | 0.57 |
| 244_V | 282_W | 1.239 | 0.56 |
| 71_T | 94_R | 1.239 | 0.56 |
| 307_L | 311_V | 1.237 | 0.56 |
| 325_I | 333_L | 1.234 | 0.56 |
| 246_G | 270_I | 1.234 | 0.56 |
| 63_D | 68_W | 1.232 | 0.56 |
| 81_C | 392_Q | 1.225 | 0.55 |
| 304_W | 308_R | 1.219 | 0.54 |
| 148_G | 181_F | 1.216 | 0.54 |
| 242_L | 350_S | 1.216 | 0.54 |
| 357_L | 397_A | 1.214 | 0.54 |
| 413_R | 416_H | 1.214 | 0.54 |
| 246_G | 271_G | 1.213 | 0.54 |
| 184_F | 351_T | 1.211 | 0.54 |
| 167_S | 391_F | 1.208 | 0.53 |
| 172_T | 183_S | 1.205 | 0.53 |
| 361_H | 399_L | 1.203 | 0.53 |
| 177_H | 180_L | 1.201 | 0.53 |
| 347_L | 386_L | 1.195 | 0.52 |
| 168_K | 322_F | 1.189 | 0.52 |
| 393_G | 401_C | 1.189 | 0.52 |
| 174_N | 187_K | 1.184 | 0.51 |
| 264_F | 267_Y | 1.183 | 0.51 |
| 233_Y | 272_W | 1.182 | 0.51 |
| 225_R | 351_T | 1.181 | 0.51 |
| 393_G | 396_V | 1.181 | 0.51 |
| 168_K | 185_V | 1.178 | 0.51 |
| 155_A | 197_L | 1.171 | 0.50 |
| 396_V | 406_E | 1.170 | 0.50 |
| 155_A | 394_L | 1.168 | 0.50 |
| 352_L | 356_P | 1.167 | 0.49 |
| 294_C | 310_P | 1.166 | 0.49 |
| 322_F | 410_E | 1.160 | 0.49 |
| 184_F | 187_K | 1.160 | 0.49 |
| 167_S | 307_L | 1.160 | 0.49 |
| 193_V | 201_R | 1.159 | 0.49 |
| 189_S | 193_V | 1.158 | 0.49 |
| 58_C | 82_P | 1.157 | 0.49 |
| 58_C | 69_P | 1.151 | 0.48 |
| 236_V | 415_W | 1.145 | 0.47 |
| 155_A | 398_V | 1.145 | 0.47 |
| 279_V | 283_A | 1.144 | 0.47 |
| 242_L | 253_L | 1.142 | 0.47 |
| 269_G | 317_I | 1.139 | 0.47 |
| 355_I | 386_L | 1.134 | 0.46 |
| 188_A | 194_I | 1.132 | 0.46 |
| 396_V | 404_N | 1.132 | 0.46 |
| 323_V | 334_R | 1.131 | 0.46 |
| 242_L | 347_L | 1.126 | 0.46 |
| 273_G | 400_Y | 1.122 | 0.45 |
| 403_L | 407_V | 1.121 | 0.45 |
| 232_Q | 237_A | 1.119 | 0.45 |
| 333_L | 397_A | 1.119 | 0.45 |
| 169_L | 325_I | 1.118 | 0.45 |
| 358_L | 402_F | 1.114 | 0.45 |
| 159_A | 187_K | 1.113 | 0.44 |
| 35_K | 38_L | 1.110 | 0.44 |
| 350_S | 410_E | 1.110 | 0.44 |
| 238_N | 241_W | 1.109 | 0.44 |
| 295_W | 310_P | 1.109 | 0.44 |
| 381_K | 384_F | 1.107 | 0.44 |
| 356_P | 401_C | 1.107 | 0.44 |
| 171_C | 175_A | 1.107 | 0.44 |
| 193_V | 313_L | 1.106 | 0.44 |
| 174_N | 188_A | 1.102 | 0.43 |
| 178_A | 405_K | 1.101 | 0.43 |
| 59_N | 151_L | 1.100 | 0.43 |
| 253_L | 346_R | 1.099 | 0.43 |
| 252_L | 286_K | 1.097 | 0.43 |
| 309_F | 312_F | 1.092 | 0.43 |
| 74_N | 186_L | 1.091 | 0.42 |
| 185_V | 397_A | 1.089 | 0.42 |
| 247_L | 321_I | 1.089 | 0.42 |
| 294_C | 305_W | 1.088 | 0.42 |
| 338_M | 343_Y | 1.087 | 0.42 |
| 194_I | 322_F | 1.086 | 0.42 |
| 63_D | 69_P | 1.086 | 0.42 |
| 325_I | 332_K | 1.085 | 0.42 |
| 158_L | 182_A | 1.085 | 0.42 |
| 168_K | 187_K | 1.083 | 0.42 |
| 174_N | 195_D | 1.080 | 0.41 |
| 331_A | 337_Q | 1.080 | 0.41 |
| 106_W | 117_D | 1.079 | 0.41 |
| 81_C | 106_W | 1.078 | 0.41 |
| 157_L | 284_V | 1.078 | 0.41 |
| 305_W | 309_F | 1.077 | 0.41 |
| 243_L | 252_L | 1.068 | 0.40 |
| 181_F | 188_A | 1.065 | 0.40 |
| 296_T | 350_S | 1.065 | 0.40 |
| 322_F | 386_L | 1.062 | 0.40 |
| 42_Q | 287_C | 1.060 | 0.40 |
| 187_K | 322_F | 1.058 | 0.39 |
| 237_A | 267_Y | 1.058 | 0.39 |
| 58_C | 62_F | 1.054 | 0.39 |
| 100_C | 121_C | 1.053 | 0.39 |
| 61_T | 70_D | 1.053 | 0.39 |
| 61_T | 414_R | 1.052 | 0.39 |
| 245_E | 248_Y | 1.048 | 0.39 |
| 68_W | 82_P | 1.045 | 0.38 |
| 306_I | 418_W | 1.044 | 0.38 |
| 149_Y | 390_S | 1.041 | 0.38 |
| 175_A | 195_D | 1.041 | 0.38 |
| 149_Y | 159_A | 1.041 | 0.38 |
| 155_A | 381_K | 1.041 | 0.38 |
| 248_Y | 271_G | 1.040 | 0.38 |
| 382_L | 411_L | 1.039 | 0.38 |
| 249_L | 272_W | 1.038 | 0.38 |
| 244_V | 270_I | 1.036 | 0.38 |
| 255_L | 291_N | 1.033 | 0.37 |
| 62_F | 65_Y | 1.033 | 0.37 |
| 187_K | 351_T | 1.030 | 0.37 |
| 225_R | 362_E | 1.030 | 0.37 |
| 249_L | 271_G | 1.026 | 0.37 |
| 394_L | 398_V | 1.026 | 0.37 |
| 321_I | 358_L | 1.024 | 0.36 |
| 98_K | 187_K | 1.022 | 0.36 |
| 250_H | 327_Q | 1.021 | 0.36 |
| 173_R | 180_L | 1.020 | 0.36 |
| 354_L | 359_G | 1.020 | 0.36 |
| 63_D | 82_P | 1.019 | 0.36 |
| 195_D | 322_F | 1.017 | 0.36 |
| 97_F | 267_Y | 1.017 | 0.36 |
| 233_Y | 271_G | 1.015 | 0.36 |
| 174_N | 184_F | 1.012 | 0.35 |
| 242_L | 328_L | 1.012 | 0.35 |
| 184_F | 238_N | 1.011 | 0.35 |
| 174_N | 194_I | 1.010 | 0.35 |
| 146_T | 163_L | 1.008 | 0.35 |
| 183_S | 361_H | 1.007 | 0.35 |
| 370_D | 381_K | 1.007 | 0.35 |
| 136_K | 380_A | 1.003 | 0.35 |
| 364_V | 380_A | 1.002 | 0.35 |
| 191_V | 386_L | 1.001 | 0.35 |
| 347_L | 410_E | 1.001 | 0.35 |
| 187_K | 282_W | 1.001 | 0.35 |
| 267_Y | 324_R | 1.000 | 0.34 |
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 | |
| 4k5yA | 3 | 0.5304 | 100 | 0.637 | Contact Map |
| 4l6rA | 1 | 0.7987 | 100 | 0.675 | Contact Map |
| 2qkhA | 1 | 0.1971 | 100 | 0.834 | Contact Map |
| 4hj0A | 2 | 0.1929 | 100 | 0.839 | Contact Map |
| 3c5tA | 1 | 0.2138 | 100 | 0.841 | Contact Map |
| 4ersA | 1 | 0.2013 | 100 | 0.844 | Contact Map |
| 4jkvA | 2 | 0.7631 | 100 | 0.847 | Contact Map |
| 4rwfA | 1 | 0 | 99.9 | 0.854 | Contact Map |
| 4qinA | 1 | 0.6646 | 99.9 | 0.859 | Contact Map |
| 1u34A | 1 | 0.2411 | 99.9 | 0.86 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)