| MSA |
| ID: | 1488558728 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 466 (401) | ||
| Sequences: | 421 (240.7) | ||
| Seq/Len: | 1.050 | ||
| Nf(neff/√len): | 12.0 |
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: 1.050).
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 |
| 406_C | 409_N | 3.408 | 1.00 |
| 406_C | 411_E | 3.237 | 1.00 |
| 405_Y | 411_E | 2.500 | 0.99 |
| 405_Y | 409_N | 2.487 | 0.99 |
| 409_N | 412_V | 2.442 | 0.99 |
| 407_F | 411_E | 2.326 | 0.99 |
| 406_C | 412_V | 2.201 | 0.98 |
| 329_R | 332_C | 2.009 | 0.96 |
| 67_R | 77_D | 1.982 | 0.96 |
| 355_S | 390_E | 1.955 | 0.95 |
| 78_G | 84_V | 1.946 | 0.95 |
| 238_Y | 250_E | 1.945 | 0.95 |
| 70_D | 74_C | 1.865 | 0.93 |
| 65_C | 74_C | 1.831 | 0.92 |
| 327_F | 352_L | 1.800 | 0.92 |
| 166_S | 184_L | 1.779 | 0.91 |
| 250_E | 277_W | 1.764 | 0.91 |
| 406_C | 410_N | 1.749 | 0.90 |
| 65_C | 75_W | 1.726 | 0.89 |
| 178_T | 182_I | 1.654 | 0.86 |
| 154_G | 162_L | 1.651 | 0.86 |
| 291_K | 297_E | 1.644 | 0.86 |
| 189_S | 243_N | 1.643 | 0.86 |
| 405_Y | 412_V | 1.640 | 0.86 |
| 408_V | 411_E | 1.592 | 0.83 |
| 154_G | 158_S | 1.580 | 0.83 |
| 407_F | 412_V | 1.567 | 0.82 |
| 123_W | 129_C | 1.564 | 0.82 |
| 180_N | 193_R | 1.555 | 0.81 |
| 161_A | 399_L | 1.535 | 0.80 |
| 357_L | 361_P | 1.525 | 0.80 |
| 247_L | 327_F | 1.512 | 0.79 |
| 65_C | 70_D | 1.507 | 0.78 |
| 179_R | 183_H | 1.470 | 0.76 |
| 246_W | 250_E | 1.467 | 0.76 |
| 180_N | 287_W | 1.459 | 0.75 |
| 176_H | 180_N | 1.444 | 0.74 |
| 178_T | 181_Y | 1.430 | 0.73 |
| 238_Y | 277_W | 1.430 | 0.73 |
| 327_F | 355_S | 1.425 | 0.73 |
| 73_A | 86_V | 1.424 | 0.73 |
| 405_Y | 408_V | 1.420 | 0.72 |
| 198_F | 355_S | 1.414 | 0.72 |
| 193_R | 200_R | 1.387 | 0.70 |
| 405_Y | 410_N | 1.384 | 0.70 |
| 70_D | 89_P | 1.383 | 0.70 |
| 355_S | 387_L | 1.382 | 0.69 |
| 125_N | 129_C | 1.377 | 0.69 |
| 250_E | 254_L | 1.371 | 0.69 |
| 123_W | 127_S | 1.365 | 0.68 |
| 312_I | 316_I | 1.350 | 0.67 |
| 339_K | 423_W | 1.348 | 0.67 |
| 169_L | 403_I | 1.337 | 0.66 |
| 229_C | 250_E | 1.335 | 0.66 |
| 194_A | 200_R | 1.334 | 0.66 |
| 230_R | 296_D | 1.330 | 0.65 |
| 154_G | 187_F | 1.326 | 0.65 |
| 398_G | 411_E | 1.323 | 0.65 |
| 352_L | 355_S | 1.307 | 0.63 |
| 236_M | 363_L | 1.305 | 0.63 |
| 70_D | 75_W | 1.301 | 0.63 |
| 74_C | 89_P | 1.297 | 0.62 |
| 309_W | 313_R | 1.291 | 0.62 |
| 174_H | 327_F | 1.290 | 0.62 |
| 174_H | 180_N | 1.288 | 0.61 |
| 250_E | 276_G | 1.284 | 0.61 |
| 152_T | 201_D | 1.281 | 0.61 |
| 238_Y | 246_W | 1.279 | 0.61 |
| 247_L | 355_S | 1.261 | 0.59 |
| 269_F | 272_Y | 1.257 | 0.59 |
| 327_F | 415_E | 1.255 | 0.59 |
| 290_V | 311_I | 1.252 | 0.58 |
| 238_Y | 257_L | 1.239 | 0.57 |
| 402_A | 406_C | 1.236 | 0.57 |
| 65_C | 89_P | 1.234 | 0.57 |
| 398_G | 406_C | 1.225 | 0.56 |
| 398_G | 409_N | 1.222 | 0.55 |
| 238_Y | 330_V | 1.222 | 0.55 |
| 84_V | 195_L | 1.219 | 0.55 |
| 233_F | 241_A | 1.218 | 0.55 |
| 401_V | 411_E | 1.215 | 0.55 |
| 165_A | 174_H | 1.207 | 0.54 |
| 180_N | 200_R | 1.205 | 0.54 |
| 254_L | 277_W | 1.205 | 0.54 |
| 262_V | 374_M | 1.195 | 0.53 |
| 274_S | 322_V | 1.188 | 0.52 |
| 150_I | 385_I | 1.188 | 0.52 |
| 186_L | 189_S | 1.183 | 0.52 |
| 175_L | 238_Y | 1.181 | 0.52 |
| 104_Y | 128_E | 1.172 | 0.51 |
| 249_V | 287_W | 1.172 | 0.51 |
| 177_C | 193_R | 1.171 | 0.51 |
| 55_E | 316_I | 1.170 | 0.51 |
| 162_L | 187_F | 1.169 | 0.51 |
| 81_G | 198_F | 1.163 | 0.50 |
| 253_Y | 276_G | 1.162 | 0.50 |
| 65_C | 76_P | 1.160 | 0.50 |
| 255_Y | 329_R | 1.157 | 0.49 |
| 247_L | 352_L | 1.156 | 0.49 |
| 359_L | 364_G | 1.153 | 0.49 |
| 251_G | 254_L | 1.153 | 0.49 |
| 330_V | 334_V | 1.151 | 0.49 |
| 401_V | 409_N | 1.148 | 0.49 |
| 155_Y | 395_S | 1.143 | 0.48 |
| 179_R | 186_L | 1.142 | 0.48 |
| 190_F | 201_D | 1.140 | 0.48 |
| 183_H | 186_L | 1.139 | 0.48 |
| 165_A | 193_R | 1.138 | 0.48 |
| 169_L | 283_F | 1.137 | 0.48 |
| 69_F | 93_P | 1.135 | 0.47 |
| 190_F | 193_R | 1.134 | 0.47 |
| 415_E | 418_R | 1.132 | 0.47 |
| 289_I | 293_L | 1.131 | 0.47 |
| 243_N | 246_W | 1.126 | 0.46 |
| 190_F | 351_R | 1.122 | 0.46 |
| 255_Y | 260_F | 1.121 | 0.46 |
| 180_N | 194_A | 1.120 | 0.46 |
| 194_A | 201_D | 1.118 | 0.46 |
| 310_L | 317_L | 1.114 | 0.45 |
| 382_L | 386_K | 1.114 | 0.45 |
| 69_F | 263_F | 1.113 | 0.45 |
| 75_W | 89_P | 1.113 | 0.45 |
| 229_C | 238_Y | 1.113 | 0.45 |
| 111_G | 123_W | 1.111 | 0.45 |
| 190_F | 243_N | 1.107 | 0.45 |
| 251_G | 334_V | 1.106 | 0.45 |
| 252_V | 262_V | 1.106 | 0.45 |
| 249_V | 352_L | 1.098 | 0.44 |
| 151_Y | 182_I | 1.096 | 0.44 |
| 53_L | 67_R | 1.088 | 0.43 |
| 193_R | 287_W | 1.086 | 0.43 |
| 178_T | 194_A | 1.083 | 0.42 |
| 310_L | 314_L | 1.080 | 0.42 |
| 415_E | 420_W | 1.079 | 0.42 |
| 398_G | 401_V | 1.076 | 0.42 |
| 324_F | 396_F | 1.075 | 0.42 |
| 173_R | 396_F | 1.074 | 0.42 |
| 174_H | 193_R | 1.072 | 0.41 |
| 196_S | 303_N | 1.072 | 0.41 |
| 200_R | 327_F | 1.068 | 0.41 |
| 76_P | 89_P | 1.066 | 0.41 |
| 158_S | 162_L | 1.060 | 0.40 |
| 153_V | 369_V | 1.060 | 0.40 |
| 324_F | 370_F | 1.060 | 0.40 |
| 182_I | 268_I | 1.058 | 0.40 |
| 186_L | 193_R | 1.057 | 0.40 |
| 45_Y | 363_L | 1.057 | 0.40 |
| 340_A | 404_L | 1.055 | 0.40 |
| 242_A | 272_Y | 1.055 | 0.40 |
| 355_S | 415_E | 1.054 | 0.40 |
| 237_Q | 242_A | 1.054 | 0.40 |
| 364_G | 397_Q | 1.053 | 0.40 |
| 180_N | 190_F | 1.052 | 0.40 |
| 326_I | 363_L | 1.050 | 0.39 |
| 177_C | 190_F | 1.050 | 0.39 |
| 165_A | 180_N | 1.049 | 0.39 |
| 285_I | 328_V | 1.048 | 0.39 |
| 327_F | 353_A | 1.046 | 0.39 |
| 247_L | 258_L | 1.044 | 0.39 |
| 331_I | 335_V | 1.044 | 0.39 |
| 327_F | 366_H | 1.042 | 0.39 |
| 105_R | 142_E | 1.041 | 0.39 |
| 412_V | 415_E | 1.039 | 0.39 |
| 348_I | 351_R | 1.035 | 0.38 |
| 35_L | 375_D | 1.034 | 0.38 |
| 279_V | 296_D | 1.033 | 0.38 |
| 187_F | 194_A | 1.033 | 0.38 |
| 62_G | 73_A | 1.032 | 0.38 |
| 177_C | 181_Y | 1.032 | 0.38 |
| 244_Y | 291_K | 1.030 | 0.38 |
| 404_L | 411_E | 1.030 | 0.38 |
| 419_S | 423_W | 1.030 | 0.38 |
| 78_G | 86_V | 1.028 | 0.38 |
| 178_T | 189_S | 1.028 | 0.38 |
| 238_Y | 254_L | 1.027 | 0.37 |
| 311_I | 315_P | 1.023 | 0.37 |
| 300_W | 315_P | 1.021 | 0.37 |
| 251_G | 323_N | 1.017 | 0.37 |
| 282_L | 399_L | 1.017 | 0.37 |
| 360_I | 391_L | 1.017 | 0.37 |
| 181_Y | 201_D | 1.015 | 0.36 |
| 358_T | 400_M | 1.015 | 0.36 |
| 180_N | 186_L | 1.011 | 0.36 |
| 35_L | 38_T | 1.011 | 0.36 |
| 182_I | 310_L | 1.011 | 0.36 |
| 53_L | 244_Y | 1.010 | 0.36 |
| 272_Y | 339_K | 1.008 | 0.36 |
| 301_T | 355_S | 1.005 | 0.36 |
| 248_L | 355_S | 1.004 | 0.35 |
| 198_F | 390_E | 1.002 | 0.35 |
| 190_F | 200_R | 1.002 | 0.35 |
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 | |
| 4k5yA | 3 | 0.5429 | 100 | 0.64 | Contact Map |
| 4l6rA | 1 | 0.8262 | 100 | 0.696 | Contact Map |
| 3c5tA | 1 | 0.2232 | 100 | 0.84 | Contact Map |
| 4jkvA | 2 | 0.7876 | 100 | 0.842 | Contact Map |
| 4hj0A | 2 | 0.1974 | 99.9 | 0.848 | Contact Map |
| 4ersA | 1 | 0.206 | 99.9 | 0.849 | Contact Map |
| 4rwfA | 1 | 0 | 99.9 | 0.852 | Contact Map |
| 4qinA | 1 | 0.691 | 99.9 | 0.855 | Contact Map |
| 2qkhA | 1 | 0.2017 | 99.9 | 0.855 | Contact Map |
| 1u34A | 1 | 0.2532 | 99.9 | 0.861 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)