| T0814 23-419 -force run |
| ID: | 1405039972 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 397 (391) | ||
| Sequences: | 231 (205.3) | ||
| Seq/Len: | 0.591 | ||
| Nf(neff/√len): | 10.4 |
Jackhmmer Results: (2014_04_16)
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: 0.591).
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 |
| 326_N | 333_E | 5.934 | 1.00 |
| 60_N | 64_T | 4.074 | 1.00 |
| 138_E | 388_R | 3.494 | 1.00 |
| 255_D | 347_Y | 3.098 | 1.00 |
| 380_R | 387_D | 2.687 | 0.99 |
| 145_A | 375_I | 2.663 | 0.99 |
| 164_F | 375_I | 2.424 | 0.97 |
| 112_S | 138_E | 2.380 | 0.96 |
| 268_D | 370_Q | 2.241 | 0.95 |
| 52_Y | 129_I | 2.097 | 0.92 |
| 323_M | 334_K | 2.062 | 0.91 |
| 305_S | 322_K | 2.024 | 0.90 |
| 173_I | 180_L | 1.984 | 0.88 |
| 374_S | 392_V | 1.890 | 0.85 |
| 44_G | 52_Y | 1.886 | 0.85 |
| 119_V | 130_F | 1.882 | 0.84 |
| 135_S | 389_L | 1.876 | 0.84 |
| 60_N | 386_Y | 1.838 | 0.83 |
| 189_R | 192_N | 1.816 | 0.81 |
| 249_N | 293_H | 1.740 | 0.77 |
| 222_E | 370_Q | 1.732 | 0.77 |
| 18_V | 40_I | 1.713 | 0.76 |
| 90_G | 323_M | 1.700 | 0.75 |
| 18_V | 132_A | 1.696 | 0.75 |
| 58_H | 66_S | 1.681 | 0.74 |
| 307_Y | 321_S | 1.646 | 0.72 |
| 238_V | 252_L | 1.645 | 0.72 |
| 222_E | 270_D | 1.628 | 0.71 |
| 376_Y | 389_L | 1.628 | 0.71 |
| 18_V | 38_I | 1.622 | 0.70 |
| 318_D | 321_S | 1.570 | 0.67 |
| 381_P | 384_A | 1.530 | 0.64 |
| 181_K | 380_R | 1.529 | 0.64 |
| 66_S | 176_P | 1.516 | 0.63 |
| 135_S | 376_Y | 1.511 | 0.62 |
| 222_E | 268_D | 1.496 | 0.61 |
| 197_L | 215_L | 1.459 | 0.58 |
| 40_I | 132_A | 1.453 | 0.58 |
| 180_L | 207_I | 1.448 | 0.57 |
| 231_N | 290_Y | 1.446 | 0.57 |
| 112_S | 162_V | 1.434 | 0.56 |
| 143_I | 377_V | 1.432 | 0.56 |
| 72_E | 385_R | 1.420 | 0.55 |
| 180_L | 377_V | 1.420 | 0.55 |
| 141_V | 171_F | 1.411 | 0.54 |
| 41_N | 284_D | 1.399 | 0.53 |
| 258_R | 363_E | 1.393 | 0.53 |
| 275_I | 304_G | 1.356 | 0.50 |
| 223_Y | 322_K | 1.353 | 0.50 |
| 270_D | 370_Q | 1.348 | 0.49 |
| 185_Y | 190_R | 1.344 | 0.49 |
| 219_A | 367_Y | 1.344 | 0.49 |
| 70_P | 78_Q | 1.333 | 0.48 |
| 254_T | 295_T | 1.325 | 0.47 |
| 154_D | 159_H | 1.318 | 0.47 |
| 111_V | 288_D | 1.317 | 0.47 |
| 129_I | 143_I | 1.309 | 0.46 |
| 185_Y | 376_Y | 1.307 | 0.46 |
| 191_D | 377_V | 1.304 | 0.46 |
| 313_F | 321_S | 1.294 | 0.45 |
| 100_L | 117_I | 1.279 | 0.44 |
| 16_L | 40_I | 1.256 | 0.42 |
| 149_G | 156_N | 1.251 | 0.42 |
| 307_Y | 322_K | 1.248 | 0.41 |
| 184_V | 325_Y | 1.246 | 0.41 |
| 160_Q | 371_N | 1.246 | 0.41 |
| 44_G | 117_I | 1.244 | 0.41 |
| 140_V | 219_A | 1.243 | 0.41 |
| 57_V | 118_Q | 1.238 | 0.41 |
| 277_C | 280_C | 1.224 | 0.39 |
| 248_Y | 367_Y | 1.215 | 0.39 |
| 31_A | 308_L | 1.214 | 0.39 |
| 173_I | 179_D | 1.210 | 0.38 |
| 54_Y | 104_N | 1.208 | 0.38 |
| 30_I | 38_I | 1.207 | 0.38 |
| 60_N | 387_D | 1.203 | 0.38 |
| 338_L | 343_Y | 1.202 | 0.38 |
| 149_G | 229_L | 1.191 | 0.37 |
| 234_N | 238_V | 1.190 | 0.37 |
| 109_F | 262_T | 1.187 | 0.37 |
| 56_V | 158_S | 1.178 | 0.36 |
| 54_Y | 76_G | 1.178 | 0.36 |
| 131_T | 214_N | 1.177 | 0.36 |
| 308_L | 336_V | 1.170 | 0.35 |
| 71_I | 265_Y | 1.169 | 0.35 |
| 72_E | 287_A | 1.167 | 0.35 |
| 75_N | 108_Q | 1.166 | 0.35 |
| 329_T | 333_E | 1.163 | 0.35 |
| 294_F | 338_L | 1.158 | 0.35 |
| 228_F | 290_Y | 1.158 | 0.35 |
| 321_S | 336_V | 1.156 | 0.34 |
| 230_S | 288_D | 1.154 | 0.34 |
| 194_V | 238_V | 1.151 | 0.34 |
| 119_V | 287_A | 1.147 | 0.34 |
| 185_Y | 374_S | 1.142 | 0.33 |
| 95_Y | 191_D | 1.133 | 0.33 |
| 161_Q | 216_I | 1.130 | 0.32 |
| 52_Y | 130_F | 1.128 | 0.32 |
| 296_L | 362_I | 1.128 | 0.32 |
| 182_I | 279_D | 1.127 | 0.32 |
| 84_D | 99_R | 1.126 | 0.32 |
| 166_I | 391_G | 1.123 | 0.32 |
| 193_A | 196_D | 1.119 | 0.32 |
| 44_G | 190_R | 1.119 | 0.32 |
| 33_G | 144_S | 1.116 | 0.32 |
| 55_N | 86_A | 1.113 | 0.31 |
| 261_G | 295_T | 1.113 | 0.31 |
| 8_V | 39_E | 1.112 | 0.31 |
| 144_S | 338_L | 1.109 | 0.31 |
| 143_I | 375_I | 1.109 | 0.31 |
| 293_H | 343_Y | 1.107 | 0.31 |
| 62_D | 168_N | 1.105 | 0.31 |
| 171_F | 379_Y | 1.105 | 0.31 |
| 15_T | 173_I | 1.102 | 0.31 |
| 145_A | 164_F | 1.099 | 0.30 |
| 13_I | 322_K | 1.098 | 0.30 |
| 166_I | 254_T | 1.094 | 0.30 |
| 176_P | 181_K | 1.093 | 0.30 |
| 225_R | 342_S | 1.086 | 0.29 |
| 229_L | 342_S | 1.085 | 0.29 |
| 18_V | 227_E | 1.084 | 0.29 |
| 224_R | 363_E | 1.084 | 0.29 |
| 166_I | 377_V | 1.084 | 0.29 |
| 105_D | 166_I | 1.079 | 0.29 |
| 102_L | 109_F | 1.078 | 0.29 |
| 154_D | 347_Y | 1.077 | 0.29 |
| 79_G | 111_V | 1.075 | 0.29 |
| 85_F | 181_K | 1.073 | 0.29 |
| 116_A | 184_V | 1.072 | 0.29 |
| 16_L | 229_L | 1.067 | 0.28 |
| 344_N | 381_P | 1.063 | 0.28 |
| 164_F | 182_I | 1.063 | 0.28 |
| 135_S | 385_R | 1.061 | 0.28 |
| 223_Y | 276_R | 1.061 | 0.28 |
| 191_D | 348_L | 1.059 | 0.28 |
| 165_N | 240_N | 1.059 | 0.28 |
| 116_A | 256_Y | 1.057 | 0.28 |
| 64_T | 324_G | 1.053 | 0.27 |
| 73_Y | 136_V | 1.050 | 0.27 |
| 67_Q | 381_P | 1.049 | 0.27 |
| 76_G | 104_N | 1.047 | 0.27 |
| 119_V | 202_I | 1.046 | 0.27 |
| 258_R | 347_Y | 1.044 | 0.27 |
| 32_L | 115_Y | 1.041 | 0.27 |
| 291_I | 335_A | 1.040 | 0.26 |
| 306_V | 336_V | 1.037 | 0.26 |
| 15_T | 169_K | 1.035 | 0.26 |
| 223_Y | 315_N | 1.034 | 0.26 |
| 143_I | 393_T | 1.034 | 0.26 |
| 191_D | 353_G | 1.032 | 0.26 |
| 64_T | 328_E | 1.032 | 0.26 |
| 146_S | 163_S | 1.031 | 0.26 |
| 16_L | 223_Y | 1.029 | 0.26 |
| 109_F | 230_S | 1.028 | 0.26 |
| 381_P | 388_R | 1.026 | 0.26 |
| 54_Y | 265_Y | 1.025 | 0.26 |
| 99_R | 337_L | 1.021 | 0.25 |
| 13_I | 52_Y | 1.021 | 0.25 |
| 60_N | 212_N | 1.017 | 0.25 |
| 145_A | 169_K | 1.015 | 0.25 |
| 60_N | 380_R | 1.014 | 0.25 |
| 227_E | 266_D | 1.012 | 0.25 |
| 32_L | 140_V | 1.002 | 0.24 |
| 192_N | 377_V | 1.001 | 0.24 |
| 13_I | 44_G | 1.000 | 0.24 |
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 | |
| 4aefA | 2 | 0.2846 | 96.3 | 0.954 | Contact Map |
| 2qlvB | 2 | 0.2166 | 96 | 0.955 | Contact Map |
| 4aeeA | 2 | 0.3023 | 96 | 0.956 | Contact Map |
| 2lu3A | 1 | 0.262 | 95.6 | 0.957 | Contact Map |
| 1ac0A | 1 | 0.2469 | 94.8 | 0.959 | Contact Map |
| 1z0nA | 3 | 0.2166 | 93.8 | 0.961 | Contact Map |
| 4cfeB | 2 | 0.2292 | 91.9 | 0.963 | Contact Map |
| 2z0bA | 6 | 0.262 | 88.4 | 0.966 | Contact Map |
| 1m7xA | 4 | 0.3023 | 70.7 | 0.972 | Contact Map |
| 1ea9C | 2 | 0.3123 | 58.6 | 0.974 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)