| MSA |
| ID: | 1490035666 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 466 (401) | ||
| Sequences: | 448 (259.7) | ||
| Seq/Len: | 1.117 | ||
| Nf(neff/√len): | 13.0 |
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: 1.117).
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 | 3.350 | 1.00 |
| 406_C | 411_E | 3.077 | 1.00 |
| 405_Y | 409_N | 2.369 | 0.99 |
| 405_Y | 411_E | 2.347 | 0.99 |
| 409_N | 412_V | 2.299 | 0.99 |
| 329_R | 332_C | 2.190 | 0.98 |
| 407_F | 411_E | 2.169 | 0.98 |
| 406_C | 412_V | 2.047 | 0.97 |
| 70_D | 74_C | 1.950 | 0.96 |
| 238_Y | 250_E | 1.950 | 0.96 |
| 355_S | 390_E | 1.927 | 0.95 |
| 65_C | 74_C | 1.920 | 0.95 |
| 67_R | 77_D | 1.913 | 0.95 |
| 166_S | 184_L | 1.903 | 0.95 |
| 78_G | 84_V | 1.832 | 0.93 |
| 65_C | 75_W | 1.764 | 0.91 |
| 327_F | 352_L | 1.757 | 0.91 |
| 250_E | 277_W | 1.726 | 0.90 |
| 154_G | 162_L | 1.720 | 0.90 |
| 154_G | 158_S | 1.656 | 0.88 |
| 189_S | 243_N | 1.654 | 0.88 |
| 406_C | 410_N | 1.652 | 0.87 |
| 291_K | 297_E | 1.652 | 0.87 |
| 123_W | 129_C | 1.629 | 0.86 |
| 65_C | 70_D | 1.595 | 0.85 |
| 178_T | 182_I | 1.583 | 0.84 |
| 180_N | 193_R | 1.571 | 0.84 |
| 179_R | 183_H | 1.542 | 0.82 |
| 180_N | 287_W | 1.520 | 0.81 |
| 246_W | 250_E | 1.505 | 0.80 |
| 198_F | 355_S | 1.482 | 0.78 |
| 357_L | 361_P | 1.476 | 0.78 |
| 125_N | 129_C | 1.467 | 0.77 |
| 247_L | 327_F | 1.465 | 0.77 |
| 408_V | 411_E | 1.456 | 0.77 |
| 169_L | 403_I | 1.450 | 0.76 |
| 250_E | 254_L | 1.429 | 0.75 |
| 405_Y | 412_V | 1.429 | 0.75 |
| 73_A | 86_V | 1.413 | 0.74 |
| 355_S | 387_L | 1.412 | 0.74 |
| 174_H | 180_N | 1.405 | 0.73 |
| 70_D | 89_P | 1.400 | 0.73 |
| 407_F | 412_V | 1.391 | 0.72 |
| 229_C | 250_E | 1.385 | 0.72 |
| 178_T | 181_Y | 1.380 | 0.71 |
| 405_Y | 408_V | 1.376 | 0.71 |
| 327_F | 355_S | 1.374 | 0.71 |
| 236_M | 363_L | 1.372 | 0.70 |
| 158_S | 162_L | 1.361 | 0.70 |
| 152_T | 201_D | 1.347 | 0.68 |
| 161_A | 399_L | 1.334 | 0.67 |
| 70_D | 75_W | 1.330 | 0.67 |
| 238_Y | 277_W | 1.323 | 0.66 |
| 247_L | 355_S | 1.319 | 0.66 |
| 176_H | 180_N | 1.316 | 0.66 |
| 123_W | 127_S | 1.315 | 0.66 |
| 81_G | 198_F | 1.312 | 0.66 |
| 312_I | 316_I | 1.312 | 0.66 |
| 250_E | 276_G | 1.310 | 0.65 |
| 74_C | 89_P | 1.308 | 0.65 |
| 255_Y | 329_R | 1.301 | 0.65 |
| 174_H | 327_F | 1.301 | 0.65 |
| 175_L | 238_Y | 1.297 | 0.64 |
| 193_R | 200_R | 1.288 | 0.63 |
| 194_A | 200_R | 1.283 | 0.63 |
| 398_G | 409_N | 1.279 | 0.63 |
| 230_R | 296_D | 1.273 | 0.62 |
| 238_Y | 246_W | 1.273 | 0.62 |
| 398_G | 411_E | 1.268 | 0.62 |
| 65_C | 89_P | 1.253 | 0.60 |
| 405_Y | 410_N | 1.253 | 0.60 |
| 269_F | 272_Y | 1.247 | 0.60 |
| 327_F | 415_E | 1.246 | 0.60 |
| 177_C | 190_F | 1.242 | 0.59 |
| 352_L | 355_S | 1.240 | 0.59 |
| 169_L | 283_F | 1.235 | 0.59 |
| 309_W | 313_R | 1.224 | 0.58 |
| 233_F | 241_A | 1.222 | 0.57 |
| 249_V | 287_W | 1.222 | 0.57 |
| 251_G | 254_L | 1.220 | 0.57 |
| 190_F | 193_R | 1.219 | 0.57 |
| 177_C | 193_R | 1.217 | 0.57 |
| 151_Y | 155_Y | 1.211 | 0.56 |
| 65_C | 76_P | 1.210 | 0.56 |
| 69_F | 263_F | 1.209 | 0.56 |
| 165_A | 193_R | 1.209 | 0.56 |
| 399_L | 403_I | 1.201 | 0.55 |
| 180_N | 194_A | 1.197 | 0.55 |
| 398_G | 406_C | 1.192 | 0.55 |
| 69_F | 93_P | 1.183 | 0.54 |
| 179_R | 186_L | 1.183 | 0.54 |
| 359_L | 364_G | 1.182 | 0.54 |
| 183_H | 186_L | 1.180 | 0.53 |
| 324_F | 396_F | 1.178 | 0.53 |
| 339_K | 423_W | 1.176 | 0.53 |
| 254_L | 277_W | 1.176 | 0.53 |
| 53_L | 67_R | 1.171 | 0.53 |
| 155_Y | 395_S | 1.171 | 0.53 |
| 262_V | 374_M | 1.171 | 0.53 |
| 238_Y | 257_L | 1.169 | 0.52 |
| 401_V | 409_N | 1.167 | 0.52 |
| 327_F | 366_H | 1.166 | 0.52 |
| 354_K | 425_L | 1.165 | 0.52 |
| 290_V | 311_I | 1.160 | 0.51 |
| 199_I | 318_F | 1.159 | 0.51 |
| 110_E | 285_I | 1.159 | 0.51 |
| 253_Y | 276_G | 1.152 | 0.51 |
| 165_A | 174_H | 1.150 | 0.51 |
| 190_F | 243_N | 1.147 | 0.50 |
| 238_Y | 330_V | 1.139 | 0.49 |
| 310_L | 314_L | 1.139 | 0.49 |
| 180_N | 200_R | 1.133 | 0.49 |
| 243_N | 277_W | 1.128 | 0.48 |
| 251_G | 334_V | 1.125 | 0.48 |
| 382_L | 386_K | 1.122 | 0.48 |
| 111_G | 123_W | 1.121 | 0.48 |
| 229_C | 238_Y | 1.119 | 0.48 |
| 155_Y | 165_A | 1.118 | 0.47 |
| 186_L | 189_S | 1.115 | 0.47 |
| 76_P | 89_P | 1.115 | 0.47 |
| 415_E | 418_R | 1.112 | 0.47 |
| 274_S | 322_V | 1.112 | 0.47 |
| 84_V | 195_L | 1.112 | 0.47 |
| 289_I | 293_L | 1.111 | 0.47 |
| 178_T | 194_A | 1.106 | 0.46 |
| 154_G | 187_F | 1.106 | 0.46 |
| 247_L | 352_L | 1.101 | 0.46 |
| 412_V | 415_E | 1.100 | 0.46 |
| 364_G | 397_Q | 1.097 | 0.45 |
| 62_G | 73_A | 1.093 | 0.45 |
| 392_S | 400_M | 1.092 | 0.45 |
| 154_G | 168_I | 1.092 | 0.45 |
| 401_V | 411_E | 1.088 | 0.45 |
| 163_V | 420_W | 1.087 | 0.45 |
| 153_V | 369_V | 1.085 | 0.44 |
| 35_L | 38_T | 1.084 | 0.44 |
| 104_Y | 128_E | 1.079 | 0.44 |
| 279_V | 296_D | 1.079 | 0.44 |
| 402_A | 406_C | 1.077 | 0.44 |
| 355_S | 415_E | 1.076 | 0.44 |
| 282_L | 399_L | 1.076 | 0.44 |
| 189_S | 366_H | 1.075 | 0.43 |
| 75_W | 89_P | 1.071 | 0.43 |
| 158_S | 172_F | 1.070 | 0.43 |
| 178_T | 189_S | 1.070 | 0.43 |
| 353_A | 396_F | 1.069 | 0.43 |
| 207_M | 210_T | 1.065 | 0.42 |
| 193_R | 287_W | 1.065 | 0.42 |
| 243_N | 246_W | 1.064 | 0.42 |
| 358_T | 400_M | 1.064 | 0.42 |
| 197_V | 201_D | 1.063 | 0.42 |
| 174_H | 193_R | 1.061 | 0.42 |
| 69_F | 388_F | 1.060 | 0.42 |
| 252_V | 326_I | 1.059 | 0.42 |
| 230_R | 356_T | 1.059 | 0.42 |
| 237_Q | 242_A | 1.057 | 0.42 |
| 340_A | 404_L | 1.056 | 0.42 |
| 182_I | 234_L | 1.054 | 0.41 |
| 330_V | 402_A | 1.052 | 0.41 |
| 249_V | 352_L | 1.049 | 0.41 |
| 196_S | 303_N | 1.048 | 0.41 |
| 255_Y | 260_F | 1.042 | 0.40 |
| 326_I | 363_L | 1.040 | 0.40 |
| 415_E | 420_W | 1.039 | 0.40 |
| 177_C | 181_Y | 1.037 | 0.40 |
| 238_Y | 254_L | 1.036 | 0.40 |
| 247_L | 258_L | 1.036 | 0.40 |
| 180_N | 190_F | 1.035 | 0.40 |
| 191_I | 402_A | 1.034 | 0.40 |
| 398_G | 401_V | 1.031 | 0.39 |
| 68_T | 77_D | 1.029 | 0.39 |
| 360_I | 391_L | 1.029 | 0.39 |
| 84_V | 261_S | 1.028 | 0.39 |
| 163_V | 167_A | 1.028 | 0.39 |
| 150_I | 385_I | 1.018 | 0.38 |
| 356_T | 401_V | 1.018 | 0.38 |
| 250_E | 253_Y | 1.018 | 0.38 |
| 78_G | 86_V | 1.018 | 0.38 |
| 348_I | 351_R | 1.013 | 0.38 |
| 413_Q | 418_R | 1.013 | 0.38 |
| 200_R | 327_F | 1.013 | 0.38 |
| 229_C | 244_Y | 1.012 | 0.38 |
| 338_L | 402_A | 1.011 | 0.38 |
| 194_A | 201_D | 1.011 | 0.38 |
| 214_Q | 289_I | 1.010 | 0.37 |
| 55_E | 316_I | 1.009 | 0.37 |
| 238_Y | 272_Y | 1.008 | 0.37 |
| 285_I | 328_V | 1.007 | 0.37 |
| 397_Q | 409_N | 1.005 | 0.37 |
| 195_L | 418_R | 1.004 | 0.37 |
| 154_G | 165_A | 1.004 | 0.37 |
| 310_L | 317_L | 1.003 | 0.37 |
| 251_G | 323_N | 1.001 | 0.37 |
| 191_I | 354_K | 1.001 | 0.37 |
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 | 0.634 | Contact Map |
| 4l6rA | 1 | 0.8262 | 100 | 0.688 | Contact Map |
| 3c5tA | 1 | 0.2232 | 100 | 0.838 | Contact Map |
| 4jkvA | 2 | 0.824 | 100 | 0.839 | Contact Map |
| 4hj0A | 2 | 0.1974 | 99.9 | 0.845 | Contact Map |
| 4ersA | 1 | 0.206 | 99.9 | 0.847 | Contact Map |
| 4rwfA | 1 | 0 | 99.9 | 0.848 | Contact Map |
| 2qkhA | 1 | 0.2017 | 99.9 | 0.852 | Contact Map |
| 4qinA | 1 | 0.6545 | 99.9 | 0.852 | Contact Map |
| 1u34A | 1 | 0.2532 | 99.9 | 0.86 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)