| Francisella tularensis large sub |
| ID: | 1517304688 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 514 (432) | ||
| Sequences: | 608 (284.3) | ||
| Seq/Len: | 1.407 | ||
| Nf(neff/√len): | 13.7 |
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: 1.407).
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 |
| 97_N | 279_F | 5.655 | 1.00 |
| 175_L | 301_V | 4.828 | 1.00 |
| 242_F | 251_I | 4.088 | 1.00 |
| 260_L | 294_G | 3.273 | 1.00 |
| 291_Y | 332_C | 3.083 | 1.00 |
| 177_L | 298_I | 2.828 | 1.00 |
| 266_P | 280_N | 2.559 | 1.00 |
| 205_I | 300_L | 2.337 | 0.99 |
| 251_I | 383_A | 2.300 | 0.99 |
| 96_V | 99_I | 2.278 | 0.99 |
| 242_F | 383_A | 2.276 | 0.99 |
| 201_H | 250_Y | 2.243 | 0.99 |
| 252_G | 382_S | 2.176 | 0.99 |
| 241_D | 373_S | 2.171 | 0.99 |
| 134_K | 137_E | 2.152 | 0.99 |
| 173_A | 304_M | 2.104 | 0.98 |
| 116_Q | 120_Q | 2.063 | 0.98 |
| 331_A | 342_T | 2.003 | 0.98 |
| 303_N | 306_R | 2.001 | 0.98 |
| 288_N | 343_K | 1.994 | 0.98 |
| 257_D | 347_N | 1.929 | 0.97 |
| 127_E | 169_E | 1.916 | 0.97 |
| 212_F | 363_L | 1.884 | 0.96 |
| 176_G | 204_F | 1.881 | 0.96 |
| 184_T | 262_Q | 1.876 | 0.96 |
| 110_Q | 292_L | 1.862 | 0.96 |
| 132_D | 137_E | 1.812 | 0.95 |
| 129_S | 171_Y | 1.751 | 0.94 |
| 92_I | 96_V | 1.711 | 0.93 |
| 244_N | 385_K | 1.698 | 0.93 |
| 254_T | 296_A | 1.682 | 0.92 |
| 403_N | 492_E | 1.681 | 0.92 |
| 107_A | 179_N | 1.669 | 0.92 |
| 442_I | 467_I | 1.625 | 0.90 |
| 287_K | 290_S | 1.570 | 0.88 |
| 110_Q | 294_G | 1.564 | 0.88 |
| 447_T | 452_P | 1.550 | 0.87 |
| 180_F | 189_W | 1.525 | 0.86 |
| 140_Y | 272_Q | 1.491 | 0.84 |
| 430_D | 433_S | 1.476 | 0.84 |
| 265_N | 268_N | 1.471 | 0.83 |
| 285_Y | 290_S | 1.456 | 0.82 |
| 154_F | 193_M | 1.452 | 0.82 |
| 316_Y | 454_P | 1.446 | 0.82 |
| 160_V | 351_A | 1.434 | 0.81 |
| 124_D | 228_E | 1.423 | 0.80 |
| 380_V | 405_S | 1.408 | 0.79 |
| 94_L | 279_F | 1.401 | 0.79 |
| 117_E | 121_E | 1.398 | 0.79 |
| 252_G | 364_I | 1.397 | 0.79 |
| 198_K | 247_V | 1.396 | 0.79 |
| 282_F | 290_S | 1.391 | 0.78 |
| 193_M | 204_F | 1.387 | 0.78 |
| 356_L | 360_N | 1.380 | 0.78 |
| 258_F | 294_G | 1.378 | 0.77 |
| 318_R | 490_Q | 1.375 | 0.77 |
| 87_V | 90_K | 1.375 | 0.77 |
| 213_F | 363_L | 1.367 | 0.77 |
| 365_P | 382_S | 1.361 | 0.76 |
| 245_L | 296_A | 1.344 | 0.75 |
| 90_K | 98_S | 1.340 | 0.75 |
| 413_I | 485_V | 1.331 | 0.74 |
| 288_N | 332_C | 1.330 | 0.74 |
| 450_Y | 463_R | 1.322 | 0.73 |
| 450_Y | 457_M | 1.321 | 0.73 |
| 143_E | 188_I | 1.318 | 0.73 |
| 114_K | 298_I | 1.306 | 0.72 |
| 90_K | 94_L | 1.305 | 0.72 |
| 218_L | 485_V | 1.303 | 0.72 |
| 97_N | 101_S | 1.299 | 0.71 |
| 158_V | 420_V | 1.287 | 0.70 |
| 141_D | 213_F | 1.283 | 0.70 |
| 208_I | 212_F | 1.278 | 0.69 |
| 88_I | 92_I | 1.277 | 0.69 |
| 417_I | 483_I | 1.276 | 0.69 |
| 238_E | 463_R | 1.272 | 0.69 |
| 389_F | 444_E | 1.266 | 0.68 |
| 478_W | 493_G | 1.255 | 0.67 |
| 103_D | 118_V | 1.253 | 0.67 |
| 166_Y | 201_H | 1.248 | 0.67 |
| 157_K | 161_S | 1.241 | 0.66 |
| 176_G | 297_S | 1.239 | 0.66 |
| 435_Q | 439_S | 1.228 | 0.65 |
| 163_F | 250_Y | 1.226 | 0.65 |
| 175_L | 297_S | 1.219 | 0.64 |
| 464_N | 486_I | 1.217 | 0.64 |
| 359_A | 379_S | 1.216 | 0.64 |
| 85_I | 107_A | 1.214 | 0.64 |
| 265_N | 280_N | 1.214 | 0.64 |
| 128_V | 172_G | 1.198 | 0.62 |
| 178_Y | 202_A | 1.190 | 0.61 |
| 106_R | 292_L | 1.181 | 0.61 |
| 214_G | 236_Y | 1.174 | 0.60 |
| 249_A | 401_I | 1.172 | 0.60 |
| 430_D | 486_I | 1.170 | 0.59 |
| 397_N | 469_V | 1.169 | 0.59 |
| 228_E | 361_I | 1.167 | 0.59 |
| 172_G | 314_F | 1.162 | 0.59 |
| 359_A | 382_S | 1.154 | 0.58 |
| 387_E | 435_Q | 1.154 | 0.58 |
| 326_V | 366_F | 1.152 | 0.58 |
| 389_F | 398_S | 1.141 | 0.57 |
| 85_I | 382_S | 1.132 | 0.56 |
| 99_I | 252_G | 1.127 | 0.55 |
| 332_C | 347_N | 1.126 | 0.55 |
| 180_F | 190_L | 1.123 | 0.55 |
| 165_Q | 351_A | 1.123 | 0.55 |
| 433_S | 486_I | 1.123 | 0.55 |
| 448_T | 457_M | 1.120 | 0.54 |
| 258_F | 299_H | 1.114 | 0.54 |
| 371_G | 486_I | 1.114 | 0.54 |
| 354_M | 357_S | 1.113 | 0.54 |
| 130_I | 336_N | 1.113 | 0.54 |
| 108_L | 206_A | 1.110 | 0.53 |
| 99_I | 269_N | 1.107 | 0.53 |
| 175_L | 207_S | 1.107 | 0.53 |
| 236_Y | 498_M | 1.103 | 0.53 |
| 133_V | 393_F | 1.098 | 0.52 |
| 365_P | 417_I | 1.095 | 0.52 |
| 314_F | 408_M | 1.089 | 0.51 |
| 193_M | 200_S | 1.088 | 0.51 |
| 180_F | 370_K | 1.088 | 0.51 |
| 148_D | 195_M | 1.087 | 0.51 |
| 113_L | 194_G | 1.085 | 0.51 |
| 325_Y | 372_T | 1.083 | 0.51 |
| 103_D | 290_S | 1.081 | 0.51 |
| 93_D | 97_N | 1.081 | 0.51 |
| 96_V | 100_I | 1.072 | 0.50 |
| 260_L | 292_L | 1.071 | 0.50 |
| 405_S | 492_E | 1.068 | 0.49 |
| 471_T | 506_P | 1.068 | 0.49 |
| 160_V | 424_K | 1.066 | 0.49 |
| 163_F | 431_V | 1.059 | 0.48 |
| 380_V | 498_M | 1.057 | 0.48 |
| 417_I | 438_L | 1.056 | 0.48 |
| 141_D | 148_D | 1.056 | 0.48 |
| 447_T | 456_E | 1.054 | 0.48 |
| 191_T | 383_A | 1.050 | 0.47 |
| 163_F | 208_I | 1.049 | 0.47 |
| 176_G | 193_M | 1.048 | 0.47 |
| 114_K | 464_N | 1.047 | 0.47 |
| 103_D | 187_I | 1.046 | 0.47 |
| 100_I | 105_F | 1.046 | 0.47 |
| 315_Q | 409_C | 1.045 | 0.47 |
| 219_S | 383_A | 1.045 | 0.47 |
| 187_I | 383_A | 1.045 | 0.47 |
| 132_D | 208_I | 1.045 | 0.47 |
| 300_L | 413_I | 1.043 | 0.47 |
| 386_V | 402_A | 1.042 | 0.47 |
| 100_I | 107_A | 1.037 | 0.46 |
| 92_I | 275_L | 1.036 | 0.46 |
| 130_I | 237_K | 1.036 | 0.46 |
| 325_Y | 369_E | 1.032 | 0.46 |
| 119_C | 420_V | 1.032 | 0.46 |
| 215_V | 229_A | 1.031 | 0.45 |
| 103_D | 289_E | 1.031 | 0.45 |
| 319_G | 324_G | 1.030 | 0.45 |
| 148_D | 238_E | 1.030 | 0.45 |
| 128_V | 498_M | 1.029 | 0.45 |
| 190_L | 251_I | 1.029 | 0.45 |
| 166_Y | 325_Y | 1.026 | 0.45 |
| 300_L | 382_S | 1.026 | 0.45 |
| 449_V | 452_P | 1.024 | 0.45 |
| 176_G | 295_P | 1.022 | 0.45 |
| 151_S | 350_F | 1.020 | 0.44 |
| 215_V | 220_E | 1.019 | 0.44 |
| 94_L | 136_E | 1.018 | 0.44 |
| 318_R | 492_E | 1.017 | 0.44 |
| 474_G | 502_T | 1.017 | 0.44 |
| 126_V | 305_M | 1.015 | 0.44 |
| 119_C | 128_V | 1.014 | 0.44 |
| 488_H | 504_L | 1.014 | 0.44 |
| 492_E | 496_T | 1.013 | 0.44 |
| 194_G | 198_K | 1.009 | 0.43 |
| 129_S | 467_I | 1.008 | 0.43 |
| 128_V | 314_F | 1.007 | 0.43 |
| 320_V | 376_C | 1.007 | 0.43 |
| 397_N | 499_T | 1.005 | 0.43 |
| 307_S | 431_V | 1.003 | 0.43 |
| 124_D | 486_I | 1.003 | 0.43 |
| 294_G | 379_S | 1.003 | 0.43 |
| 164_D | 351_A | 1.000 | 0.42 |
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 | |
| 3j9oB | 6 | 0.821 | 100 | 0.167 | Contact Map |
| 2jxfA | 1 | 0.0428 | 29.4 | 0.985 | Contact Map |
| 3cuqA | 1 | 0.2062 | 10.3 | 0.988 | Contact Map |
| 4flnA | 3 | 0.1401 | 7.9 | 0.988 | Contact Map |
| 3jstA | 2 | 0.1109 | 7.3 | 0.989 | Contact Map |
| 2ebbA | 1 | 0.1051 | 6.8 | 0.989 | Contact Map |
| 3cuqB | 1 | 0.1926 | 6.4 | 0.989 | Contact Map |
| 2v6uA | 2 | 0.1167 | 6.2 | 0.989 | Contact Map |
| 3j7aJ | 1 | 0.1673 | 5.8 | 0.989 | Contact Map |
| 4bpe3 | 1 | 0.1654 | 5.5 | 0.989 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)