| epaz |
| ID: | 1499158636 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 375 (367) | ||
| Sequences: | 2080 (1169) | ||
| Seq/Len: | 5.668 | ||
| Nf(neff/√len): | 61.0 |
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: 5.668).
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 |
| 179_D | 199_K | 8.419 | 1.00 |
| 95_L | 139_V | 4.836 | 1.00 |
| 131_D | 166_R | 3.871 | 1.00 |
| 269_Q | 296_H | 3.754 | 1.00 |
| 33_E | 37_Q | 3.722 | 1.00 |
| 303_V | 333_V | 3.664 | 1.00 |
| 34_I | 38_E | 3.558 | 1.00 |
| 274_S | 302_D | 3.386 | 1.00 |
| 115_E | 132_R | 3.046 | 1.00 |
| 280_V | 313_E | 2.915 | 1.00 |
| 236_M | 299_M | 2.899 | 1.00 |
| 92_Y | 100_K | 2.750 | 1.00 |
| 320_L | 324_F | 2.671 | 1.00 |
| 272_A | 301_F | 2.621 | 1.00 |
| 305_V | 337_V | 2.589 | 1.00 |
| 229_H | 232_T | 2.558 | 1.00 |
| 300_L | 331_L | 2.518 | 1.00 |
| 180_E | 183_R | 2.493 | 1.00 |
| 274_S | 277_T | 2.398 | 1.00 |
| 134_K | 168_I | 2.363 | 1.00 |
| 196_D | 199_K | 2.237 | 1.00 |
| 6_P | 36_Y | 2.213 | 1.00 |
| 224_W | 333_V | 2.165 | 1.00 |
| 236_M | 334_S | 2.158 | 1.00 |
| 291_L | 298_V | 2.155 | 1.00 |
| 42_S | 71_V | 2.141 | 1.00 |
| 185_G | 188_R | 2.140 | 1.00 |
| 21_P | 26_K | 2.103 | 1.00 |
| 192_L | 196_D | 2.056 | 1.00 |
| 276_T | 280_V | 2.017 | 1.00 |
| 31_R | 203_D | 2.017 | 1.00 |
| 182_Y | 185_G | 1.955 | 1.00 |
| 11_L | 26_K | 1.901 | 1.00 |
| 101_Q | 111_R | 1.884 | 1.00 |
| 170_L | 202_C | 1.873 | 1.00 |
| 99_R | 138_D | 1.861 | 1.00 |
| 9_Q | 13_A | 1.832 | 1.00 |
| 289_I | 323_E | 1.832 | 1.00 |
| 71_V | 169_T | 1.817 | 1.00 |
| 28_A | 76_M | 1.815 | 1.00 |
| 115_E | 136_E | 1.786 | 1.00 |
| 255_E | 260_P | 1.765 | 1.00 |
| 292_S | 324_F | 1.760 | 1.00 |
| 146_F | 176_I | 1.760 | 1.00 |
| 101_Q | 136_E | 1.758 | 1.00 |
| 277_T | 281_D | 1.754 | 1.00 |
| 290_A | 293_R | 1.705 | 1.00 |
| 298_V | 324_F | 1.702 | 1.00 |
| 160_M | 194_A | 1.665 | 1.00 |
| 142_F | 172_A | 1.638 | 0.99 |
| 236_M | 301_F | 1.627 | 0.99 |
| 85_T | 326_E | 1.627 | 0.99 |
| 279_C | 320_L | 1.620 | 0.99 |
| 237_D | 272_A | 1.596 | 0.99 |
| 265_G | 272_A | 1.579 | 0.99 |
| 182_Y | 188_R | 1.574 | 0.99 |
| 116_L | 126_L | 1.569 | 0.99 |
| 147_V | 156_L | 1.556 | 0.99 |
| 88_M | 141_C | 1.540 | 0.99 |
| 77_W | 177_P | 1.533 | 0.99 |
| 196_D | 200_Q | 1.533 | 0.99 |
| 163_L | 168_I | 1.509 | 0.99 |
| 266_V | 295_F | 1.481 | 0.99 |
| 124_D | 158_G | 1.480 | 0.99 |
| 261_L | 291_L | 1.477 | 0.99 |
| 5_T | 8_S | 1.475 | 0.99 |
| 112_V | 155_L | 1.458 | 0.99 |
| 318_I | 348_L | 1.433 | 0.98 |
| 101_Q | 140_L | 1.430 | 0.98 |
| 364_S | 367_Y | 1.428 | 0.98 |
| 253_T | 260_P | 1.410 | 0.98 |
| 233_R | 302_D | 1.409 | 0.98 |
| 315_R | 351_E | 1.380 | 0.98 |
| 88_M | 173_T | 1.379 | 0.98 |
| 7_T | 11_L | 1.375 | 0.98 |
| 5_T | 33_E | 1.371 | 0.98 |
| 111_R | 136_E | 1.371 | 0.98 |
| 105_F | 142_F | 1.368 | 0.98 |
| 263_T | 273_V | 1.367 | 0.98 |
| 304_P | 313_E | 1.358 | 0.97 |
| 235_Q | 239_L | 1.344 | 0.97 |
| 11_L | 15_N | 1.335 | 0.97 |
| 39_L | 169_T | 1.331 | 0.97 |
| 261_L | 277_T | 1.328 | 0.97 |
| 19_H | 86_W | 1.303 | 0.96 |
| 243_L | 299_M | 1.299 | 0.96 |
| 224_W | 335_A | 1.294 | 0.96 |
| 111_R | 115_E | 1.291 | 0.96 |
| 338_P | 341_E | 1.280 | 0.96 |
| 178_P | 204_V | 1.268 | 0.96 |
| 42_S | 138_D | 1.267 | 0.96 |
| 252_P | 295_F | 1.265 | 0.96 |
| 176_I | 350_F | 1.263 | 0.96 |
| 7_T | 30_S | 1.250 | 0.95 |
| 188_R | 192_L | 1.242 | 0.95 |
| 137_T | 140_L | 1.229 | 0.95 |
| 300_L | 320_L | 1.224 | 0.95 |
| 263_T | 271_L | 1.216 | 0.94 |
| 73_G | 172_A | 1.201 | 0.94 |
| 146_F | 319_A | 1.193 | 0.93 |
| 338_P | 363_Q | 1.188 | 0.93 |
| 177_P | 180_E | 1.178 | 0.93 |
| 150_I | 154_M | 1.177 | 0.93 |
| 225_L | 232_T | 1.177 | 0.93 |
| 26_K | 30_S | 1.174 | 0.93 |
| 253_T | 262_A | 1.168 | 0.93 |
| 237_D | 301_F | 1.163 | 0.92 |
| 12_K | 16_E | 1.161 | 0.92 |
| 164_F | 202_C | 1.139 | 0.91 |
| 33_E | 36_Y | 1.133 | 0.91 |
| 176_I | 319_A | 1.129 | 0.91 |
| 23_D | 27_E | 1.129 | 0.91 |
| 35_I | 169_T | 1.128 | 0.91 |
| 101_Q | 115_E | 1.121 | 0.90 |
| 7_T | 33_E | 1.120 | 0.90 |
| 161_K | 165_A | 1.119 | 0.90 |
| 147_V | 191_F | 1.117 | 0.90 |
| 89_D | 102_R | 1.114 | 0.90 |
| 354_R | 357_S | 1.111 | 0.90 |
| 145_F | 172_A | 1.111 | 0.90 |
| 297_T | 330_K | 1.102 | 0.89 |
| 118_A | 132_R | 1.094 | 0.89 |
| 264_M | 274_S | 1.088 | 0.89 |
| 36_Y | 94_S | 1.088 | 0.89 |
| 310_M | 313_E | 1.087 | 0.88 |
| 113_H | 152_D | 1.087 | 0.88 |
| 285_Q | 319_A | 1.086 | 0.88 |
| 337_V | 341_E | 1.085 | 0.88 |
| 278_L | 300_L | 1.080 | 0.88 |
| 235_Q | 238_K | 1.079 | 0.88 |
| 53_M | 56_V | 1.077 | 0.88 |
| 40_I | 96_P | 1.074 | 0.88 |
| 335_A | 339_L | 1.072 | 0.88 |
| 211_V | 216_R | 1.070 | 0.87 |
| 365_E | 369_K | 1.061 | 0.87 |
| 335_A | 342_I | 1.055 | 0.86 |
| 264_M | 277_T | 1.054 | 0.86 |
| 91_F | 141_C | 1.053 | 0.86 |
| 153_A | 182_Y | 1.050 | 0.86 |
| 103_L | 142_F | 1.049 | 0.86 |
| 282_A | 326_E | 1.045 | 0.86 |
| 240_W | 272_A | 1.043 | 0.86 |
| 85_T | 176_I | 1.040 | 0.85 |
| 237_D | 241_L | 1.039 | 0.85 |
| 347_R | 351_E | 1.037 | 0.85 |
| 306_M | 314_A | 1.037 | 0.85 |
| 97_G | 138_D | 1.037 | 0.85 |
| 103_L | 111_R | 1.034 | 0.85 |
| 76_M | 87_L | 1.025 | 0.84 |
| 9_Q | 12_K | 1.022 | 0.84 |
| 254_L | 295_F | 1.017 | 0.84 |
| 305_V | 336_E | 1.012 | 0.83 |
| 225_L | 235_Q | 1.002 | 0.82 |
| 321_V | 331_L | 1.002 | 0.82 |
| 56_V | 60_W | 1.001 | 0.82 |
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 | |
| 2w58A | 2 | 0.4773 | 99.7 | 0.861 | Contact Map |
| 4m4wJ | 6 | 0.5093 | 99.7 | 0.862 | Contact Map |
| 2qgzA | 1 | 0.4293 | 99.6 | 0.87 | Contact Map |
| 3ec2A | 1 | 0.4427 | 99.6 | 0.871 | Contact Map |
| 3bosA | 2 | 0.5867 | 99.1 | 0.899 | Contact Map |
| 1u0jA | 1 | 0.5467 | 99 | 0.904 | Contact Map |
| 2qz4A | 1 | 0.5787 | 98.9 | 0.909 | Contact Map |
| 1tueA | 6 | 0.512 | 98.8 | 0.911 | Contact Map |
| 4cr2L | 1 | 0.6293 | 98.8 | 0.911 | Contact Map |
| 1l8qA | 1 | 0.784 | 98.8 | 0.911 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)