| hknoali |
| ID: | 1500207465 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 371 (344) | ||
| Sequences: | 680 (467.6) | ||
| Seq/Len: | 1.977 | ||
| Nf(neff/√len): | 25.2 |
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: 1.977).
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 |
| 202_S | 223_V | 3.372 | 1.00 |
| 191_L | 234_V | 2.532 | 1.00 |
| 292_V | 304_C | 2.420 | 1.00 |
| 203_D | 228_R | 2.234 | 1.00 |
| 192_G | 234_V | 2.174 | 1.00 |
| 288_L | 317_I | 2.120 | 0.99 |
| 345_L | 364_M | 2.101 | 0.99 |
| 303_T | 322_D | 2.095 | 0.99 |
| 286_M | 289_K | 1.978 | 0.99 |
| 314_E | 365_A | 1.973 | 0.99 |
| 284_L | 317_I | 1.961 | 0.99 |
| 291_A | 362_L | 1.959 | 0.99 |
| 302_K | 322_D | 1.936 | 0.99 |
| 238_V | 335_G | 1.928 | 0.99 |
| 295_V | 304_C | 1.919 | 0.98 |
| 179_E | 182_R | 1.844 | 0.98 |
| 179_E | 344_R | 1.746 | 0.97 |
| 293_T | 297_K | 1.731 | 0.97 |
| 263_I | 301_A | 1.625 | 0.95 |
| 194_K | 230_S | 1.588 | 0.94 |
| 292_V | 306_V | 1.549 | 0.93 |
| 187_L | 203_D | 1.547 | 0.93 |
| 301_A | 322_D | 1.518 | 0.92 |
| 263_I | 299_S | 1.518 | 0.92 |
| 318_T | 361_K | 1.516 | 0.91 |
| 290_E | 293_T | 1.516 | 0.91 |
| 292_V | 296_V | 1.513 | 0.91 |
| 291_A | 341_M | 1.500 | 0.91 |
| 202_S | 220_L | 1.493 | 0.91 |
| 220_L | 223_V | 1.492 | 0.91 |
| 320_S | 361_K | 1.484 | 0.90 |
| 199_G | 224_Q | 1.473 | 0.90 |
| 76_T | 113_I | 1.455 | 0.89 |
| 287_C | 341_M | 1.443 | 0.89 |
| 49_F | 53_Y | 1.432 | 0.88 |
| 354_I | 360_T | 1.422 | 0.88 |
| 323_G | 359_G | 1.421 | 0.88 |
| 326_K | 360_T | 1.417 | 0.87 |
| 290_E | 340_G | 1.410 | 0.87 |
| 290_E | 297_K | 1.407 | 0.87 |
| 276_I | 315_V | 1.407 | 0.87 |
| 185_R | 235_R | 1.402 | 0.87 |
| 172_A | 176_K | 1.374 | 0.85 |
| 321_D | 359_G | 1.372 | 0.85 |
| 206_R | 223_V | 1.354 | 0.84 |
| 193_Q | 326_K | 1.346 | 0.83 |
| 321_D | 360_T | 1.336 | 0.83 |
| 186_D | 191_L | 1.328 | 0.82 |
| 266_I | 305_R | 1.325 | 0.82 |
| 167_A | 171_I | 1.323 | 0.82 |
| 241_M | 292_V | 1.320 | 0.82 |
| 192_G | 293_T | 1.317 | 0.82 |
| 341_M | 352_L | 1.313 | 0.81 |
| 291_A | 319_V | 1.313 | 0.81 |
| 343_E | 347_F | 1.309 | 0.81 |
| 342_R | 346_E | 1.308 | 0.81 |
| 287_C | 364_M | 1.305 | 0.81 |
| 301_A | 323_G | 1.305 | 0.81 |
| 98_I | 205_A | 1.298 | 0.80 |
| 194_K | 234_V | 1.295 | 0.80 |
| 273_P | 310_Q | 1.295 | 0.80 |
| 179_E | 185_R | 1.293 | 0.80 |
| 31_W | 34_S | 1.289 | 0.80 |
| 235_R | 344_R | 1.280 | 0.79 |
| 321_D | 325_F | 1.268 | 0.78 |
| 22_F | 26_P | 1.251 | 0.77 |
| 199_G | 340_G | 1.242 | 0.76 |
| 355_D | 358_N | 1.241 | 0.76 |
| 92_A | 192_G | 1.234 | 0.75 |
| 287_C | 291_A | 1.226 | 0.75 |
| 287_C | 345_L | 1.218 | 0.74 |
| 115_A | 303_T | 1.218 | 0.74 |
| 29_F | 35_S | 1.213 | 0.74 |
| 202_S | 224_Q | 1.213 | 0.74 |
| 192_G | 335_G | 1.207 | 0.73 |
| 87_F | 91_I | 1.205 | 0.73 |
| 277_S | 280_N | 1.201 | 0.73 |
| 351_S | 365_A | 1.199 | 0.72 |
| 258_L | 292_V | 1.199 | 0.72 |
| 204_L | 250_E | 1.197 | 0.72 |
| 193_Q | 293_T | 1.192 | 0.72 |
| 31_W | 35_S | 1.184 | 0.71 |
| 269_E | 274_E | 1.181 | 0.71 |
| 200_L | 237_I | 1.176 | 0.70 |
| 185_R | 340_G | 1.173 | 0.70 |
| 235_R | 323_G | 1.156 | 0.68 |
| 268_E | 305_R | 1.155 | 0.68 |
| 192_G | 336_H | 1.153 | 0.68 |
| 290_E | 294_N | 1.145 | 0.67 |
| 224_Q | 238_V | 1.138 | 0.67 |
| 299_S | 304_C | 1.132 | 0.66 |
| 206_R | 224_Q | 1.128 | 0.66 |
| 250_E | 289_K | 1.124 | 0.65 |
| 192_G | 203_D | 1.118 | 0.65 |
| 193_Q | 231_L | 1.115 | 0.64 |
| 274_E | 308_I | 1.109 | 0.64 |
| 201_K | 223_V | 1.108 | 0.64 |
| 158_E | 335_G | 1.108 | 0.64 |
| 190_T | 231_L | 1.106 | 0.63 |
| 231_L | 235_R | 1.106 | 0.63 |
| 180_R | 235_R | 1.103 | 0.63 |
| 199_G | 202_S | 1.103 | 0.63 |
| 159_R | 366_I | 1.098 | 0.63 |
| 271_K | 310_Q | 1.097 | 0.62 |
| 203_D | 323_G | 1.089 | 0.62 |
| 289_K | 335_G | 1.084 | 0.61 |
| 27_F | 31_W | 1.078 | 0.60 |
| 317_I | 346_E | 1.076 | 0.60 |
| 191_L | 216_A | 1.073 | 0.60 |
| 186_D | 237_I | 1.071 | 0.60 |
| 155_K | 191_L | 1.063 | 0.59 |
| 25_L | 29_F | 1.062 | 0.59 |
| 267_Y | 305_R | 1.062 | 0.59 |
| 343_E | 366_I | 1.061 | 0.59 |
| 302_K | 365_A | 1.060 | 0.59 |
| 76_T | 353_H | 1.059 | 0.58 |
| 112_L | 116_A | 1.058 | 0.58 |
| 186_D | 242_K | 1.058 | 0.58 |
| 75_S | 116_A | 1.056 | 0.58 |
| 315_V | 368_N | 1.055 | 0.58 |
| 293_T | 360_T | 1.055 | 0.58 |
| 248_K | 312_W | 1.054 | 0.58 |
| 102_V | 141_L | 1.053 | 0.58 |
| 179_E | 235_R | 1.052 | 0.58 |
| 316_V | 365_A | 1.050 | 0.57 |
| 338_L | 341_M | 1.047 | 0.57 |
| 205_A | 219_E | 1.046 | 0.57 |
| 232_N | 299_S | 1.046 | 0.57 |
| 184_A | 291_A | 1.045 | 0.57 |
| 207_K | 231_L | 1.044 | 0.57 |
| 241_M | 304_C | 1.043 | 0.57 |
| 340_G | 343_E | 1.042 | 0.57 |
| 117_V | 205_A | 1.042 | 0.57 |
| 325_F | 360_T | 1.040 | 0.56 |
| 303_T | 349_N | 1.035 | 0.56 |
| 316_V | 362_L | 1.034 | 0.56 |
| 313_K | 353_H | 1.033 | 0.56 |
| 196_S | 204_L | 1.032 | 0.55 |
| 268_E | 307_D | 1.032 | 0.55 |
| 118_A | 367_P | 1.030 | 0.55 |
| 301_A | 321_D | 1.030 | 0.55 |
| 164_L | 171_I | 1.028 | 0.55 |
| 124_V | 319_V | 1.025 | 0.55 |
| 192_G | 289_K | 1.024 | 0.55 |
| 219_E | 223_V | 1.024 | 0.55 |
| 21_I | 28_Y | 1.023 | 0.54 |
| 154_R | 313_K | 1.023 | 0.54 |
| 203_D | 234_V | 1.022 | 0.54 |
| 51_S | 55_F | 1.021 | 0.54 |
| 190_T | 193_Q | 1.021 | 0.54 |
| 345_L | 350_G | 1.019 | 0.54 |
| 201_K | 219_E | 1.014 | 0.54 |
| 24_I | 30_I | 1.011 | 0.53 |
| 115_A | 291_A | 1.010 | 0.53 |
| 191_L | 230_S | 1.006 | 0.53 |
| 51_S | 54_R | 1.005 | 0.53 |
| 189_D | 235_R | 1.003 | 0.52 |
| 279_L | 347_F | 1.001 | 0.52 |
| 205_A | 251_L | 1.001 | 0.52 |
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 | |
| 3ehhA | 2 | 0.5283 | 100 | 0.6 | Contact Map |
| 4r39A | 4 | 0.504 | 99.9 | 0.751 | Contact Map |
| 4bixA | 2 | 0.5499 | 99.8 | 0.767 | Contact Map |
| 2c2aA | 1 | 0.5606 | 99.8 | 0.772 | Contact Map |
| 4i5sA | 2 | 0.6954 | 99.8 | 0.774 | Contact Map |
| 4q20A | 2 | 0.5445 | 99.8 | 0.776 | Contact Map |
| 3ehgA | 1 | 0.3369 | 99.8 | 0.782 | Contact Map |
| 3zxqA | 2 | 0.3288 | 99.8 | 0.783 | Contact Map |
| 3d36A | 2 | 0.5256 | 99.7 | 0.785 | Contact Map |
| 3a0rA | 1 | 0.8113 | 99.7 | 0.787 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)