| rbcL |
| ID: | 1429047506 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 479 (450) | ||
| Sequences: | 757 (390.4) | ||
| Seq/Len: | 1.682 | ||
| Nf(neff/√len): | 18.4 |
Jackhmmer Results: (2015_01_07)
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: 1.682).
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 |
| 422_V | 443_E | 4.636 | 1.00 |
| 411_W | 446_R | 4.047 | 1.00 |
| 422_V | 441_G | 3.440 | 1.00 |
| 224_A | 228_S | 2.692 | 1.00 |
| 35_D | 102_A | 2.665 | 1.00 |
| 137_D | 316_K | 2.634 | 1.00 |
| 50_P | 97_F | 2.550 | 1.00 |
| 38_A | 135_L | 2.548 | 1.00 |
| 187_R | 191_E | 2.529 | 1.00 |
| 258_R | 289_L | 2.483 | 1.00 |
| 257_A | 265_V | 2.480 | 1.00 |
| 257_A | 262_V | 2.261 | 0.99 |
| 384_V | 419_A | 2.189 | 0.99 |
| 436_D | 439_V | 2.118 | 0.99 |
| 437_L | 441_G | 2.097 | 0.99 |
| 190_Y | 228_S | 2.046 | 0.99 |
| 37_L | 100_Y | 2.013 | 0.99 |
| 37_L | 139_R | 1.992 | 0.98 |
| 190_Y | 227_K | 1.976 | 0.98 |
| 183_K | 216_D | 1.975 | 0.98 |
| 190_Y | 224_A | 1.901 | 0.98 |
| 85_Y | 102_A | 1.899 | 0.98 |
| 37_L | 102_A | 1.831 | 0.97 |
| 116_M | 144_Y | 1.827 | 0.97 |
| 216_D | 219_L | 1.806 | 0.97 |
| 86_H | 100_Y | 1.769 | 0.96 |
| 426_A | 437_L | 1.741 | 0.95 |
| 442_N | 445_I | 1.705 | 0.95 |
| 439_V | 445_I | 1.693 | 0.95 |
| 267_H | 277_N | 1.634 | 0.93 |
| 190_Y | 194_R | 1.626 | 0.93 |
| 297_M | 309_M | 1.622 | 0.93 |
| 193_L | 236_K | 1.608 | 0.92 |
| 431_R | 437_L | 1.589 | 0.92 |
| 88_E | 98_I | 1.582 | 0.91 |
| 116_M | 140_I | 1.553 | 0.90 |
| 227_K | 230_A | 1.549 | 0.90 |
| 34_T | 143_A | 1.543 | 0.90 |
| 191_E | 414_A | 1.538 | 0.90 |
| 445_I | 449_C | 1.532 | 0.90 |
| 229_Q | 235_I | 1.529 | 0.90 |
| 195_G | 417_A | 1.527 | 0.89 |
| 227_K | 231_E | 1.511 | 0.89 |
| 271_T | 297_M | 1.503 | 0.88 |
| 145_T | 320_L | 1.485 | 0.88 |
| 407_L | 413_N | 1.469 | 0.87 |
| 152_P | 281_S | 1.460 | 0.86 |
| 418_V | 443_E | 1.457 | 0.86 |
| 446_R | 449_C | 1.449 | 0.86 |
| 218_F | 240_L | 1.448 | 0.86 |
| 223_E | 227_K | 1.447 | 0.86 |
| 194_R | 228_S | 1.421 | 0.84 |
| 152_P | 288_G | 1.420 | 0.84 |
| 444_I | 448_A | 1.397 | 0.83 |
| 412_G | 416_G | 1.397 | 0.83 |
| 245_G | 249_E | 1.387 | 0.82 |
| 60_E | 123_N | 1.385 | 0.82 |
| 422_V | 437_L | 1.370 | 0.81 |
| 156_Q | 373_G | 1.367 | 0.81 |
| 155_I | 350_R | 1.366 | 0.81 |
| 444_I | 447_E | 1.363 | 0.81 |
| 225_I | 238_H | 1.361 | 0.81 |
| 206_V | 209_Q | 1.360 | 0.81 |
| 277_N | 323_G | 1.358 | 0.80 |
| 100_Y | 139_R | 1.354 | 0.80 |
| 239_Y | 264_I | 1.343 | 0.79 |
| 182_A | 212_M | 1.336 | 0.79 |
| 153_H | 290_L | 1.333 | 0.79 |
| 219_L | 256_F | 1.328 | 0.78 |
| 327_H | 379_S | 1.326 | 0.78 |
| 375_L | 399_V | 1.320 | 0.78 |
| 118_T | 268_D | 1.318 | 0.78 |
| 62_S | 82_G | 1.314 | 0.77 |
| 39_A | 139_R | 1.311 | 0.77 |
| 156_Q | 160_D | 1.309 | 0.77 |
| 325_H | 399_V | 1.309 | 0.77 |
| 385_W | 452_S | 1.300 | 0.76 |
| 41_R | 96_Q | 1.297 | 0.76 |
| 173_T | 239_Y | 1.281 | 0.75 |
| 442_N | 446_R | 1.276 | 0.74 |
| 434_G | 444_I | 1.264 | 0.73 |
| 157_V | 324_D | 1.262 | 0.73 |
| 126_G | 333_G | 1.261 | 0.73 |
| 167_R | 198_D | 1.258 | 0.73 |
| 213_R | 216_D | 1.257 | 0.73 |
| 112_S | 115_N | 1.251 | 0.72 |
| 50_P | 99_A | 1.237 | 0.71 |
| 185_Y | 221_C | 1.235 | 0.71 |
| 295_R | 327_H | 1.228 | 0.70 |
| 254_A | 280_L | 1.226 | 0.70 |
| 60_E | 335_L | 1.221 | 0.70 |
| 164_K | 167_R | 1.220 | 0.70 |
| 426_A | 438_A | 1.217 | 0.69 |
| 124_V | 379_S | 1.214 | 0.69 |
| 256_F | 260_L | 1.212 | 0.69 |
| 189_V | 225_I | 1.211 | 0.69 |
| 177_K | 329_G | 1.211 | 0.69 |
| 171_G | 295_R | 1.204 | 0.68 |
| 61_S | 176_P | 1.204 | 0.68 |
| 292_H | 295_R | 1.204 | 0.68 |
| 431_R | 440_E | 1.199 | 0.68 |
| 249_E | 253_R | 1.199 | 0.68 |
| 64_G | 104_P | 1.194 | 0.67 |
| 81_K | 274_F | 1.188 | 0.67 |
| 270_L | 274_F | 1.184 | 0.66 |
| 234_E | 421_R | 1.184 | 0.66 |
| 254_A | 287_N | 1.180 | 0.66 |
| 268_D | 296_A | 1.176 | 0.65 |
| 421_R | 425_E | 1.167 | 0.65 |
| 283_Y | 287_N | 1.163 | 0.64 |
| 103_Y | 333_G | 1.160 | 0.64 |
| 292_H | 327_H | 1.159 | 0.64 |
| 226_Y | 229_Q | 1.158 | 0.64 |
| 278_T | 282_H | 1.158 | 0.64 |
| 292_H | 325_H | 1.156 | 0.64 |
| 38_A | 119_S | 1.155 | 0.63 |
| 404_G | 408_G | 1.153 | 0.63 |
| 402_F | 420_N | 1.153 | 0.63 |
| 432_N | 435_R | 1.151 | 0.63 |
| 431_R | 444_I | 1.145 | 0.62 |
| 206_V | 212_M | 1.145 | 0.62 |
| 436_D | 440_E | 1.141 | 0.62 |
| 325_H | 377_V | 1.138 | 0.62 |
| 266_M | 329_G | 1.130 | 0.61 |
| 193_L | 228_S | 1.121 | 0.60 |
| 164_K | 168_P | 1.118 | 0.60 |
| 226_Y | 230_A | 1.117 | 0.60 |
| 432_N | 436_D | 1.116 | 0.60 |
| 326_I | 349_L | 1.115 | 0.59 |
| 123_N | 334_K | 1.115 | 0.59 |
| 137_D | 150_G | 1.114 | 0.59 |
| 295_R | 334_K | 1.111 | 0.59 |
| 310_H | 399_V | 1.111 | 0.59 |
| 142_P | 340_E | 1.105 | 0.58 |
| 75_T | 259_E | 1.104 | 0.58 |
| 60_E | 327_H | 1.101 | 0.58 |
| 54_G | 101_V | 1.101 | 0.58 |
| 173_T | 402_F | 1.100 | 0.58 |
| 409_H | 412_G | 1.095 | 0.57 |
| 171_G | 292_H | 1.094 | 0.57 |
| 123_N | 327_H | 1.094 | 0.57 |
| 193_L | 225_I | 1.093 | 0.57 |
| 173_T | 379_S | 1.090 | 0.57 |
| 123_N | 266_M | 1.087 | 0.56 |
| 115_N | 118_T | 1.086 | 0.56 |
| 120_I | 138_L | 1.083 | 0.56 |
| 419_A | 451_W | 1.081 | 0.56 |
| 189_V | 380_G | 1.078 | 0.56 |
| 426_A | 434_G | 1.076 | 0.55 |
| 142_P | 259_E | 1.075 | 0.55 |
| 89_P | 95_T | 1.073 | 0.55 |
| 245_G | 253_R | 1.070 | 0.55 |
| 265_V | 290_L | 1.065 | 0.54 |
| 57_V | 130_L | 1.063 | 0.54 |
| 202_D | 217_R | 1.063 | 0.54 |
| 35_D | 85_Y | 1.060 | 0.54 |
| 60_E | 334_K | 1.059 | 0.54 |
| 208_S | 213_R | 1.059 | 0.54 |
| 434_G | 448_A | 1.058 | 0.53 |
| 262_V | 265_V | 1.058 | 0.53 |
| 59_A | 62_S | 1.058 | 0.53 |
| 105_L | 141_P | 1.057 | 0.53 |
| 146_K | 227_K | 1.057 | 0.53 |
| 248_E | 279_S | 1.055 | 0.53 |
| 101_V | 368_W | 1.055 | 0.53 |
| 55_A | 413_N | 1.055 | 0.53 |
| 442_N | 449_C | 1.053 | 0.53 |
| 409_H | 416_G | 1.049 | 0.52 |
| 105_L | 143_A | 1.043 | 0.52 |
| 171_G | 327_H | 1.043 | 0.52 |
| 89_P | 414_A | 1.041 | 0.52 |
| 86_H | 113_V | 1.040 | 0.52 |
| 67_T | 172_C | 1.039 | 0.51 |
| 431_R | 441_G | 1.038 | 0.51 |
| 83_R | 102_A | 1.037 | 0.51 |
| 292_H | 334_K | 1.036 | 0.51 |
| 153_H | 288_G | 1.036 | 0.51 |
| 150_G | 316_K | 1.035 | 0.51 |
| 208_S | 253_R | 1.033 | 0.51 |
| 115_N | 209_Q | 1.033 | 0.51 |
| 170_L | 424_L | 1.032 | 0.51 |
| 214_W | 253_R | 1.032 | 0.51 |
| 339_R | 343_L | 1.031 | 0.51 |
| 177_K | 205_N | 1.030 | 0.50 |
| 249_E | 279_S | 1.030 | 0.50 |
| 90_V | 96_Q | 1.029 | 0.50 |
| 189_V | 311_F | 1.027 | 0.50 |
| 39_A | 100_Y | 1.026 | 0.50 |
| 43_T | 96_Q | 1.021 | 0.49 |
| 384_V | 451_W | 1.020 | 0.49 |
| 86_H | 155_I | 1.020 | 0.49 |
| 171_G | 334_K | 1.019 | 0.49 |
| 254_A | 333_G | 1.018 | 0.49 |
| 195_G | 407_L | 1.017 | 0.49 |
| 204_E | 416_G | 1.016 | 0.49 |
| 208_S | 212_M | 1.014 | 0.49 |
| 296_A | 383_H | 1.013 | 0.49 |
| 87_I | 99_A | 1.012 | 0.49 |
| 293_I | 314_L | 1.011 | 0.48 |
| 91_P | 439_V | 1.010 | 0.48 |
| 387_M | 398_S | 1.010 | 0.48 |
| 84_C | 399_V | 1.009 | 0.48 |
| 414_A | 418_V | 1.008 | 0.48 |
| 115_N | 207_N | 1.006 | 0.48 |
| 125_F | 378_A | 1.006 | 0.48 |
| 68_T | 74_L | 1.006 | 0.48 |
| 38_A | 266_M | 1.005 | 0.48 |
| 190_Y | 231_E | 1.002 | 0.47 |
| 169_L | 375_L | 1.001 | 0.47 |
| 215_R | 256_F | 1.001 | 0.47 |
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 | |
| 1wddA | 2 | 0.9457 | 100 | 0.135 | Contact Map |
| 4f0hA | 1 | 0.9061 | 100 | 0.145 | Contact Map |
| 3kdnA | 10 | 0.9061 | 100 | 0.179 | Contact Map |
| 2d69A | 4 | 0.8873 | 100 | 0.198 | Contact Map |
| 2qygA | 4 | 0.8622 | 100 | 0.204 | Contact Map |
| 5rubA | 2 | 0.8768 | 100 | 0.208 | Contact Map |
| 3nwrA | 1 | 0.7975 | 100 | 0.216 | Contact Map |
| 1ykwA | 2 | 0.8309 | 100 | 0.218 | Contact Map |
| 4nasA | 4 | 0.8288 | 100 | 0.218 | Contact Map |
| 2zviA | 4 | 0.833 | 100 | 0.22 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)