| spdl1 |
| ID: | 1481302735 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 448 (435) | ||
| Sequences: | 559 (398) | ||
| Seq/Len: | 1.285 | ||
| Nf(neff/√len): | 19.1 |
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: 1.285).
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 |
| 431_L | 434_L | 3.798 | 1.00 |
| 59_K | 62_L | 2.638 | 1.00 |
| 279_Y | 282_L | 2.609 | 1.00 |
| 424_N | 427_L | 2.545 | 1.00 |
| 417_L | 420_S | 2.447 | 1.00 |
| 190_R | 195_E | 2.347 | 0.99 |
| 233_N | 236_L | 2.257 | 0.99 |
| 134_V | 137_Q | 2.174 | 0.99 |
| 239_Q | 244_L | 2.162 | 0.99 |
| 382_I | 385_T | 2.152 | 0.98 |
| 389_L | 392_Q | 2.074 | 0.98 |
| 62_L | 66_V | 1.932 | 0.96 |
| 293_M | 296_M | 1.902 | 0.96 |
| 375_L | 378_L | 1.889 | 0.96 |
| 6_I | 9_L | 1.814 | 0.94 |
| 381_E | 417_L | 1.712 | 0.92 |
| 120_L | 123_A | 1.605 | 0.88 |
| 170_L | 173_M | 1.604 | 0.88 |
| 127_E | 130_L | 1.601 | 0.88 |
| 40_Q | 45_R | 1.586 | 0.87 |
| 240_L | 243_A | 1.564 | 0.86 |
| 13_L | 16_A | 1.550 | 0.86 |
| 148_L | 151_M | 1.547 | 0.85 |
| 423_E | 428_R | 1.547 | 0.85 |
| 63_Q | 116_L | 1.533 | 0.85 |
| 4_D | 10_R | 1.523 | 0.84 |
| 36_E | 132_H | 1.515 | 0.84 |
| 58_E | 63_Q | 1.513 | 0.84 |
| 311_T | 384_S | 1.475 | 0.81 |
| 9_L | 181_K | 1.465 | 0.81 |
| 169_E | 174_E | 1.454 | 0.80 |
| 187_L | 191_Q | 1.429 | 0.79 |
| 281_S | 295_R | 1.425 | 0.78 |
| 258_F | 265_R | 1.413 | 0.77 |
| 407_E | 415_R | 1.412 | 0.77 |
| 65_E | 151_M | 1.403 | 0.77 |
| 27_G | 30_L | 1.376 | 0.75 |
| 41_L | 65_E | 1.370 | 0.74 |
| 63_Q | 244_L | 1.348 | 0.73 |
| 39_N | 43_K | 1.333 | 0.71 |
| 234_Q | 375_L | 1.324 | 0.71 |
| 9_L | 428_R | 1.318 | 0.70 |
| 88_K | 104_Q | 1.308 | 0.69 |
| 7_T | 14_K | 1.290 | 0.68 |
| 326_K | 334_L | 1.286 | 0.67 |
| 77_S | 275_M | 1.270 | 0.66 |
| 329_E | 334_L | 1.269 | 0.66 |
| 380_K | 403_A | 1.269 | 0.66 |
| 78_C | 335_G | 1.265 | 0.66 |
| 383_E | 387_G | 1.264 | 0.66 |
| 395_K | 399_E | 1.260 | 0.65 |
| 12_R | 22_K | 1.253 | 0.65 |
| 361_L | 364_N | 1.249 | 0.64 |
| 410_L | 414_E | 1.245 | 0.64 |
| 341_E | 375_L | 1.245 | 0.64 |
| 70_S | 92_E | 1.242 | 0.64 |
| 162_E | 166_L | 1.227 | 0.62 |
| 278_K | 283_K | 1.226 | 0.62 |
| 359_G | 391_I | 1.224 | 0.62 |
| 212_K | 318_R | 1.223 | 0.62 |
| 259_A | 264_R | 1.223 | 0.62 |
| 71_R | 74_E | 1.220 | 0.61 |
| 190_R | 299_Q | 1.219 | 0.61 |
| 39_N | 128_K | 1.214 | 0.61 |
| 167_Q | 407_E | 1.211 | 0.61 |
| 9_L | 389_L | 1.208 | 0.60 |
| 91_L | 94_L | 1.206 | 0.60 |
| 131_K | 136_H | 1.204 | 0.60 |
| 286_N | 289_N | 1.204 | 0.60 |
| 284_K | 304_L | 1.204 | 0.60 |
| 149_R | 157_E | 1.202 | 0.60 |
| 27_G | 31_V | 1.201 | 0.60 |
| 394_M | 403_A | 1.199 | 0.59 |
| 9_L | 236_L | 1.199 | 0.59 |
| 395_K | 408_R | 1.195 | 0.59 |
| 282_L | 406_I | 1.190 | 0.59 |
| 68_L | 74_E | 1.190 | 0.59 |
| 121_D | 366_Y | 1.188 | 0.58 |
| 84_K | 87_Q | 1.186 | 0.58 |
| 223_Y | 374_K | 1.186 | 0.58 |
| 105_E | 110_K | 1.186 | 0.58 |
| 299_Q | 431_L | 1.184 | 0.58 |
| 205_V | 208_L | 1.178 | 0.57 |
| 338_R | 341_E | 1.170 | 0.57 |
| 253_K | 260_E | 1.170 | 0.57 |
| 13_L | 17_E | 1.166 | 0.56 |
| 44_C | 48_M | 1.166 | 0.56 |
| 338_R | 342_K | 1.161 | 0.56 |
| 99_S | 102_H | 1.160 | 0.56 |
| 166_L | 200_N | 1.160 | 0.56 |
| 226_L | 283_K | 1.159 | 0.56 |
| 258_F | 268_M | 1.159 | 0.56 |
| 42_D | 46_N | 1.158 | 0.56 |
| 59_K | 85_Q | 1.157 | 0.55 |
| 228_K | 232_A | 1.156 | 0.55 |
| 141_L | 144_K | 1.155 | 0.55 |
| 79_E | 84_K | 1.154 | 0.55 |
| 401_Q | 432_D | 1.154 | 0.55 |
| 424_N | 430_K | 1.150 | 0.55 |
| 31_V | 34_Q | 1.150 | 0.55 |
| 89_M | 92_E | 1.147 | 0.54 |
| 57_Q | 149_R | 1.145 | 0.54 |
| 92_E | 96_E | 1.145 | 0.54 |
| 3_A | 119_E | 1.145 | 0.54 |
| 53_E | 57_Q | 1.145 | 0.54 |
| 367_Y | 372_Q | 1.139 | 0.54 |
| 252_S | 259_A | 1.139 | 0.54 |
| 260_E | 265_R | 1.138 | 0.54 |
| 95_E | 219_A | 1.134 | 0.53 |
| 68_L | 215_R | 1.131 | 0.53 |
| 372_Q | 379_N | 1.131 | 0.53 |
| 392_Q | 399_E | 1.126 | 0.52 |
| 20_R | 23_A | 1.120 | 0.52 |
| 311_T | 347_Y | 1.119 | 0.52 |
| 75_S | 277_V | 1.117 | 0.51 |
| 35_N | 39_N | 1.117 | 0.51 |
| 368_T | 371_L | 1.117 | 0.51 |
| 418_Q | 422_S | 1.113 | 0.51 |
| 208_L | 212_K | 1.112 | 0.51 |
| 63_Q | 85_Q | 1.111 | 0.51 |
| 428_R | 435_K | 1.109 | 0.51 |
| 302_T | 394_M | 1.108 | 0.51 |
| 72_M | 333_L | 1.105 | 0.50 |
| 55_Y | 214_E | 1.102 | 0.50 |
| 16_A | 20_R | 1.102 | 0.50 |
| 341_E | 364_N | 1.100 | 0.50 |
| 407_E | 410_L | 1.099 | 0.50 |
| 7_T | 12_R | 1.098 | 0.50 |
| 430_K | 433_E | 1.095 | 0.49 |
| 210_E | 219_A | 1.095 | 0.49 |
| 93_K | 96_E | 1.094 | 0.49 |
| 118_V | 331_K | 1.094 | 0.49 |
| 10_R | 14_K | 1.092 | 0.49 |
| 144_K | 197_L | 1.090 | 0.49 |
| 313_F | 316_Q | 1.089 | 0.49 |
| 348_D | 386_K | 1.086 | 0.48 |
| 248_L | 262_E | 1.086 | 0.48 |
| 426_K | 430_K | 1.086 | 0.48 |
| 232_A | 237_Q | 1.085 | 0.48 |
| 253_K | 258_F | 1.084 | 0.48 |
| 315_Q | 320_L | 1.084 | 0.48 |
| 151_M | 303_L | 1.084 | 0.48 |
| 18_E | 38_Q | 1.083 | 0.48 |
| 123_A | 183_E | 1.082 | 0.48 |
| 130_L | 134_V | 1.081 | 0.48 |
| 131_K | 224_N | 1.081 | 0.48 |
| 334_L | 338_R | 1.076 | 0.47 |
| 403_A | 426_K | 1.075 | 0.47 |
| 410_L | 413_N | 1.075 | 0.47 |
| 292_Q | 299_Q | 1.075 | 0.47 |
| 121_D | 124_R | 1.075 | 0.47 |
| 126_S | 130_L | 1.073 | 0.47 |
| 99_S | 103_G | 1.070 | 0.47 |
| 403_A | 406_I | 1.070 | 0.47 |
| 3_A | 236_L | 1.069 | 0.47 |
| 80_C | 423_E | 1.066 | 0.46 |
| 254_G | 258_F | 1.064 | 0.46 |
| 181_K | 203_R | 1.063 | 0.46 |
| 90_H | 93_K | 1.061 | 0.46 |
| 9_L | 166_L | 1.056 | 0.45 |
| 8_N | 241_D | 1.056 | 0.45 |
| 248_L | 252_S | 1.054 | 0.45 |
| 420_S | 424_N | 1.052 | 0.45 |
| 56_E | 60_Y | 1.051 | 0.45 |
| 309_S | 359_G | 1.051 | 0.45 |
| 340_L | 360_T | 1.051 | 0.45 |
| 405_D | 415_R | 1.050 | 0.45 |
| 84_K | 388_E | 1.048 | 0.45 |
| 223_Y | 293_M | 1.048 | 0.45 |
| 68_L | 203_R | 1.048 | 0.45 |
| 290_R | 293_M | 1.048 | 0.45 |
| 5_I | 16_A | 1.047 | 0.45 |
| 214_E | 220_V | 1.045 | 0.44 |
| 249_D | 253_K | 1.043 | 0.44 |
| 321_A | 343_F | 1.043 | 0.44 |
| 281_S | 301_A | 1.042 | 0.44 |
| 402_R | 405_D | 1.041 | 0.44 |
| 91_L | 95_E | 1.040 | 0.44 |
| 168_I | 327_N | 1.040 | 0.44 |
| 418_Q | 432_D | 1.040 | 0.44 |
| 62_L | 83_I | 1.036 | 0.43 |
| 37_L | 41_L | 1.035 | 0.43 |
| 105_E | 192_E | 1.033 | 0.43 |
| 6_I | 368_T | 1.029 | 0.43 |
| 203_R | 250_P | 1.026 | 0.42 |
| 8_N | 12_R | 1.026 | 0.42 |
| 429_A | 432_D | 1.025 | 0.42 |
| 81_E | 262_E | 1.024 | 0.42 |
| 257_L | 264_R | 1.023 | 0.42 |
| 386_K | 390_S | 1.020 | 0.42 |
| 62_L | 153_E | 1.018 | 0.42 |
| 190_R | 261_V | 1.018 | 0.42 |
| 34_Q | 37_L | 1.016 | 0.42 |
| 168_I | 172_E | 1.015 | 0.41 |
| 120_L | 427_L | 1.015 | 0.41 |
| 13_L | 185_N | 1.015 | 0.41 |
| 140_L | 180_L | 1.013 | 0.41 |
| 163_M | 431_L | 1.012 | 0.41 |
| 349_S | 403_A | 1.012 | 0.41 |
| 89_M | 218_E | 1.011 | 0.41 |
| 220_V | 255_N | 1.011 | 0.41 |
| 293_M | 297_K | 1.010 | 0.41 |
| 256_S | 264_R | 1.009 | 0.41 |
| 390_S | 408_R | 1.007 | 0.41 |
| 226_L | 229_A | 1.006 | 0.41 |
| 271_Q | 275_M | 1.005 | 0.40 |
| 95_E | 261_V | 1.001 | 0.40 |
| 81_E | 186_E | 1.001 | 0.40 |
| 110_K | 146_E | 1.001 | 0.40 |
| 351_E | 356_V | 1.000 | 0.40 |
| 10_R | 20_R | 1.000 | 0.40 |
| 275_M | 284_K | 1.000 | 0.40 |
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 | |
| 1i84S | 2 | 0.192 | 99.3 | 0.752 | Contact Map |
| 1c1gA | 4 | 0.6339 | 98.8 | 0.795 | Contact Map |
| 2dfsA | 2 | 0.3103 | 97.1 | 0.866 | Contact Map |
| 4uxvA | 1 | 0.7835 | 96.5 | 0.876 | Contact Map |
| 2v71A | 2 | 0.3348 | 96.1 | 0.881 | Contact Map |
| 4ll8A | 1 | 0.1049 | 95.8 | 0.883 | Contact Map |
| 4iloA | 2 | 0.3862 | 95.3 | 0.887 | Contact Map |
| 3na7A | 1 | 0.3996 | 92.5 | 0.9 | Contact Map |
| 4cgkA | 2 | 0.5 | 92 | 0.902 | Contact Map |
| 3ojaB | 1 | 0.2879 | 91.5 | 0.903 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)