| Q53VV3_full |
| ID: | 1379705058 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 397 (310) | ||
| Sequences: | 838 (709.9) | ||
| Seq/Len: | 2.703 | ||
| Nf(neff/√len): | 40.3 |
HHblits Results: (2013_03)
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: 2.703).
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 |
| 362_T | 370_R | 3.992 | 1.00 |
| 207_A | 217_C | 3.968 | 1.00 |
| 233_F | 247_L | 3.613 | 1.00 |
| 219_V | 233_F | 3.327 | 1.00 |
| 377_A | 380_A | 2.961 | 1.00 |
| 234_D | 252_H | 2.762 | 1.00 |
| 74_R | 108_L | 2.755 | 1.00 |
| 309_V | 361_A | 2.710 | 1.00 |
| 218_Q | 274_R | 2.682 | 1.00 |
| 310_R | 362_T | 2.573 | 1.00 |
| 339_V | 364_L | 2.566 | 1.00 |
| 216_T | 234_D | 2.398 | 1.00 |
| 308_R | 365_E | 2.322 | 1.00 |
| 149_E | 177_R | 2.268 | 1.00 |
| 354_I | 373_V | 2.267 | 1.00 |
| 219_V | 270_I | 2.123 | 1.00 |
| 308_R | 339_V | 2.043 | 1.00 |
| 310_R | 364_L | 1.981 | 0.99 |
| 231_Y | 251_N | 1.951 | 0.99 |
| 363_V | 373_V | 1.912 | 0.99 |
| 216_T | 252_H | 1.901 | 0.99 |
| 216_T | 232_R | 1.896 | 0.99 |
| 94_I | 105_V | 1.867 | 0.99 |
| 306_R | 343_E | 1.852 | 0.99 |
| 236_Y | 249_G | 1.849 | 0.99 |
| 309_V | 340_W | 1.811 | 0.99 |
| 218_Q | 232_R | 1.778 | 0.99 |
| 310_R | 337_S | 1.776 | 0.99 |
| 79_L | 135_L | 1.771 | 0.99 |
| 104_S | 107_R | 1.741 | 0.98 |
| 207_A | 270_I | 1.732 | 0.98 |
| 308_R | 341_Q | 1.725 | 0.98 |
| 231_Y | 265_L | 1.681 | 0.98 |
| 310_R | 333_L | 1.678 | 0.98 |
| 218_Q | 230_T | 1.676 | 0.98 |
| 310_R | 339_V | 1.672 | 0.98 |
| 90_P | 93_E | 1.667 | 0.98 |
| 312_S | 360_H | 1.659 | 0.97 |
| 220_T | 230_T | 1.644 | 0.97 |
| 82_L | 119_V | 1.643 | 0.97 |
| 236_Y | 280_F | 1.596 | 0.97 |
| 309_V | 354_I | 1.581 | 0.96 |
| 333_L | 337_S | 1.557 | 0.96 |
| 215_R | 277_R | 1.555 | 0.96 |
| 233_F | 249_G | 1.510 | 0.95 |
| 117_V | 135_L | 1.486 | 0.94 |
| 209_R | 213_E | 1.473 | 0.94 |
| 355_V | 376_W | 1.472 | 0.94 |
| 94_I | 238_L | 1.463 | 0.94 |
| 254_S | 265_L | 1.457 | 0.94 |
| 100_V | 105_V | 1.440 | 0.93 |
| 310_R | 370_R | 1.438 | 0.93 |
| 81_L | 98_L | 1.427 | 0.93 |
| 333_L | 339_V | 1.416 | 0.92 |
| 251_N | 265_L | 1.415 | 0.92 |
| 93_E | 96_A | 1.407 | 0.92 |
| 77_D | 81_L | 1.398 | 0.92 |
| 306_R | 341_Q | 1.394 | 0.91 |
| 313_P | 337_S | 1.370 | 0.91 |
| 92_R | 96_A | 1.360 | 0.90 |
| 270_I | 273_L | 1.358 | 0.90 |
| 371_R | 375_A | 1.339 | 0.89 |
| 377_A | 381_V | 1.339 | 0.89 |
| 331_E | 339_V | 1.332 | 0.89 |
| 330_V | 338_V | 1.331 | 0.89 |
| 95_A | 105_V | 1.319 | 0.88 |
| 79_L | 117_V | 1.318 | 0.88 |
| 311_F | 357_Y | 1.317 | 0.88 |
| 231_Y | 254_S | 1.272 | 0.86 |
| 325_H | 328_Q | 1.267 | 0.85 |
| 375_A | 379_G | 1.265 | 0.85 |
| 217_C | 238_L | 1.264 | 0.85 |
| 125_N | 132_W | 1.259 | 0.85 |
| 378_K | 382_A | 1.251 | 0.84 |
| 106_Y | 149_E | 1.239 | 0.84 |
| 359_P | 376_W | 1.238 | 0.83 |
| 109_R | 148_E | 1.220 | 0.82 |
| 307_V | 344_V | 1.217 | 0.82 |
| 207_A | 219_V | 1.216 | 0.82 |
| 231_Y | 263_K | 1.209 | 0.81 |
| 222_K | 226_G | 1.201 | 0.81 |
| 120_E | 134_R | 1.200 | 0.81 |
| 297_A | 349_D | 1.199 | 0.81 |
| 311_F | 319_I | 1.198 | 0.81 |
| 236_Y | 285_F | 1.185 | 0.80 |
| 79_L | 112_A | 1.169 | 0.78 |
| 351_V | 376_W | 1.165 | 0.78 |
| 174_L | 177_R | 1.164 | 0.78 |
| 251_N | 263_K | 1.164 | 0.78 |
| 311_F | 315_K | 1.155 | 0.77 |
| 251_N | 254_S | 1.152 | 0.77 |
| 334_P | 337_S | 1.137 | 0.76 |
| 374_V | 381_V | 1.135 | 0.75 |
| 378_K | 385_E | 1.135 | 0.75 |
| 111_K | 115_L | 1.129 | 0.75 |
| 117_V | 237_A | 1.120 | 0.74 |
| 88_G | 134_R | 1.118 | 0.74 |
| 220_T | 365_E | 1.114 | 0.73 |
| 296_R | 349_D | 1.112 | 0.73 |
| 219_V | 265_L | 1.112 | 0.73 |
| 102_R | 106_Y | 1.112 | 0.73 |
| 237_A | 287_V | 1.110 | 0.73 |
| 222_K | 271_L | 1.107 | 0.73 |
| 95_A | 100_V | 1.102 | 0.72 |
| 306_R | 365_E | 1.100 | 0.72 |
| 215_R | 275_L | 1.098 | 0.72 |
| 324_R | 340_W | 1.096 | 0.72 |
| 354_I | 361_A | 1.094 | 0.72 |
| 355_V | 380_A | 1.092 | 0.71 |
| 308_R | 364_L | 1.083 | 0.70 |
| 254_S | 263_K | 1.077 | 0.70 |
| 372_R | 375_A | 1.076 | 0.70 |
| 280_F | 290_Y | 1.075 | 0.70 |
| 220_T | 272_D | 1.073 | 0.69 |
| 367_E | 371_R | 1.068 | 0.69 |
| 363_V | 384_N | 1.065 | 0.69 |
| 109_R | 160_M | 1.064 | 0.68 |
| 280_F | 285_F | 1.054 | 0.67 |
| 214_R | 280_F | 1.049 | 0.67 |
| 99_G | 122_H | 1.044 | 0.66 |
| 320_R | 332_D | 1.043 | 0.66 |
| 220_T | 271_L | 1.042 | 0.66 |
| 125_N | 138_P | 1.039 | 0.66 |
| 250_A | 254_S | 1.032 | 0.65 |
| 101_R | 124_E | 1.030 | 0.65 |
| 132_W | 135_L | 1.029 | 0.65 |
| 120_E | 136_E | 1.028 | 0.65 |
| 228_V | 271_L | 1.023 | 0.64 |
| 358_G | 384_N | 1.020 | 0.64 |
| 113_Q | 245_L | 1.019 | 0.64 |
| 100_V | 104_S | 1.019 | 0.64 |
| 101_R | 118_W | 1.011 | 0.63 |
| 207_A | 267_L | 1.008 | 0.62 |
| 156_A | 234_D | 1.004 | 0.62 |
| 109_R | 133_M | 1.003 | 0.62 |
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 | |
| 1b4aA | 6 | 0.3325 | 98 | 0.923 | Contact Map |
| 3ke2A | 3 | 0.2469 | 97.8 | 0.927 | Contact Map |
| 2p5kA | 1 | 0.1461 | 97.8 | 0.927 | Contact Map |
| 3lapA | 6 | 0.3375 | 97.4 | 0.932 | Contact Map |
| 1xd7A | 1 | 0.272 | 97.4 | 0.933 | Contact Map |
| 4a0zA | 2 | 0.4207 | 97.3 | 0.933 | Contact Map |
| 3t8rA | 1 | 0.3023 | 97.1 | 0.935 | Contact Map |
| 2y75A | 6 | 0.3123 | 97.1 | 0.936 | Contact Map |
| 1sfuA | 2 | 0.1713 | 97.1 | 0.936 | Contact Map |
| 3k69A | 1 | 0.3401 | 97.1 | 0.936 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)