| t6ss |
| ID: | 1432886537 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 494 (485) | ||
| Sequences: | 679 (353.7) | ||
| Seq/Len: | 1.400 | ||
| Nf(neff/√len): | 16.1 |
Jackhmmer Results: (2015_01_07)
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: 1.400).
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 |
| 83_N | 263_F | 5.151 | 1.00 |
| 229_F | 238_V | 4.827 | 1.00 |
| 162_S | 284_T | 4.487 | 1.00 |
| 247_L | 277_G | 3.671 | 1.00 |
| 274_Y | 315_H | 3.221 | 1.00 |
| 164_N | 281_V | 2.618 | 1.00 |
| 163_A | 191_F | 2.515 | 1.00 |
| 238_V | 366_T | 2.449 | 1.00 |
| 160_I | 287_V | 2.369 | 0.99 |
| 253_E | 264_T | 2.366 | 0.99 |
| 73_E | 76_K | 2.254 | 0.99 |
| 239_G | 365_S | 2.222 | 0.99 |
| 192_I | 283_L | 2.184 | 0.99 |
| 102_K | 106_D | 2.182 | 0.99 |
| 228_S | 356_D | 2.163 | 0.99 |
| 231_E | 368_K | 2.150 | 0.99 |
| 141_L | 180_C | 2.148 | 0.99 |
| 188_H | 237_Y | 2.116 | 0.99 |
| 229_F | 366_T | 2.115 | 0.99 |
| 271_H | 326_K | 2.079 | 0.98 |
| 241_A | 279_A | 2.060 | 0.98 |
| 314_L | 325_T | 2.029 | 0.98 |
| 122_S | 125_D | 1.991 | 0.98 |
| 171_P | 255_T | 1.898 | 0.97 |
| 120_N | 125_D | 1.873 | 0.96 |
| 199_V | 346_F | 1.854 | 0.96 |
| 51_E | 54_A | 1.825 | 0.95 |
| 244_R | 330_E | 1.813 | 0.95 |
| 96_S | 275_L | 1.762 | 0.94 |
| 252_G | 255_T | 1.750 | 0.94 |
| 299_N | 441_P | 1.742 | 0.94 |
| 239_G | 347_I | 1.729 | 0.93 |
| 147_S | 334_T | 1.700 | 0.93 |
| 171_P | 249_L | 1.689 | 0.92 |
| 151_G | 334_T | 1.667 | 0.92 |
| 20_S | 23_D | 1.663 | 0.92 |
| 339_F | 343_E | 1.635 | 0.91 |
| 308_A | 355_S | 1.628 | 0.90 |
| 417_E | 420_D | 1.624 | 0.90 |
| 117_E | 158_Y | 1.601 | 0.89 |
| 125_D | 180_C | 1.599 | 0.89 |
| 103_F | 107_R | 1.583 | 0.89 |
| 115_R | 156_K | 1.577 | 0.88 |
| 23_D | 42_K | 1.575 | 0.88 |
| 150_Y | 237_Y | 1.569 | 0.88 |
| 429_L | 454_V | 1.567 | 0.88 |
| 390_Q | 479_M | 1.564 | 0.88 |
| 417_E | 473_R | 1.561 | 0.88 |
| 236_R | 388_G | 1.549 | 0.87 |
| 167_F | 176_L | 1.540 | 0.87 |
| 437_D | 450_R | 1.534 | 0.86 |
| 270_H | 273_R | 1.530 | 0.86 |
| 245_F | 277_G | 1.528 | 0.86 |
| 422_E | 426_N | 1.518 | 0.86 |
| 195_A | 199_V | 1.511 | 0.85 |
| 142_Y | 410_E | 1.502 | 0.85 |
| 286_R | 289_D | 1.498 | 0.85 |
| 434_S | 439_P | 1.495 | 0.85 |
| 144_L | 148_N | 1.467 | 0.83 |
| 131_E | 175_E | 1.463 | 0.83 |
| 147_S | 151_G | 1.458 | 0.82 |
| 96_S | 277_G | 1.397 | 0.79 |
| 200_F | 346_F | 1.392 | 0.78 |
| 112_E | 215_K | 1.392 | 0.78 |
| 363_A | 392_P | 1.391 | 0.78 |
| 215_K | 344_E | 1.388 | 0.78 |
| 271_H | 315_H | 1.364 | 0.76 |
| 342_S | 365_S | 1.341 | 0.74 |
| 80_S | 263_F | 1.339 | 0.74 |
| 78_L | 82_V | 1.337 | 0.74 |
| 233_E | 466_Y | 1.337 | 0.74 |
| 128_K | 259_K | 1.319 | 0.73 |
| 80_S | 84_E | 1.316 | 0.72 |
| 15_N | 18_S | 1.314 | 0.72 |
| 150_Y | 491_L | 1.304 | 0.72 |
| 89_K | 272_E | 1.304 | 0.72 |
| 109_D | 292_A | 1.300 | 0.71 |
| 369_P | 389_T | 1.290 | 0.70 |
| 172_Q | 256_V | 1.289 | 0.70 |
| 152_V | 334_T | 1.284 | 0.70 |
| 29_A | 51_E | 1.281 | 0.70 |
| 187_A | 197_P | 1.275 | 0.69 |
| 240_L | 412_I | 1.272 | 0.69 |
| 372_F | 385_Y | 1.271 | 0.69 |
| 82_V | 446_R | 1.271 | 0.69 |
| 153_F | 188_H | 1.265 | 0.68 |
| 404_I | 470_L | 1.261 | 0.68 |
| 187_A | 273_R | 1.260 | 0.68 |
| 279_A | 398_T | 1.260 | 0.68 |
| 242_L | 348_G | 1.259 | 0.68 |
| 76_K | 80_S | 1.257 | 0.67 |
| 14_A | 17_A | 1.256 | 0.67 |
| 335_E | 436_M | 1.250 | 0.67 |
| 163_A | 223_Y | 1.244 | 0.66 |
| 348_G | 404_I | 1.241 | 0.66 |
| 342_S | 363_A | 1.234 | 0.65 |
| 337_R | 340_E | 1.231 | 0.65 |
| 185_A | 234_D | 1.225 | 0.65 |
| 10_S | 14_A | 1.218 | 0.64 |
| 245_F | 282_A | 1.218 | 0.64 |
| 420_D | 473_R | 1.216 | 0.64 |
| 150_Y | 257_P | 1.214 | 0.64 |
| 145_V | 158_Y | 1.213 | 0.63 |
| 135_E | 225_R | 1.211 | 0.63 |
| 479_M | 483_F | 1.208 | 0.63 |
| 465_W | 480_G | 1.205 | 0.63 |
| 28_E | 31_L | 1.205 | 0.63 |
| 29_A | 47_A | 1.197 | 0.62 |
| 301_I | 477_K | 1.196 | 0.62 |
| 223_Y | 485_L | 1.190 | 0.61 |
| 172_Q | 257_P | 1.188 | 0.61 |
| 71_I | 74_I | 1.185 | 0.61 |
| 11_T | 15_N | 1.183 | 0.61 |
| 162_S | 287_V | 1.181 | 0.60 |
| 179_K | 182_S | 1.178 | 0.60 |
| 117_E | 454_V | 1.176 | 0.60 |
| 194_N | 241_A | 1.174 | 0.60 |
| 435_D | 439_P | 1.172 | 0.59 |
| 400_L | 472_V | 1.168 | 0.59 |
| 12_G | 16_D | 1.167 | 0.59 |
| 205_F | 472_V | 1.165 | 0.59 |
| 379_K | 382_E | 1.165 | 0.59 |
| 303_P | 359_A | 1.164 | 0.59 |
| 290_S | 418_K | 1.156 | 0.58 |
| 10_S | 13_V | 1.151 | 0.57 |
| 266_D | 273_R | 1.147 | 0.57 |
| 100_S | 247_L | 1.146 | 0.57 |
| 475_H | 491_L | 1.142 | 0.57 |
| 104_M | 285_S | 1.139 | 0.56 |
| 147_S | 411_Q | 1.135 | 0.56 |
| 161_I | 184_A | 1.133 | 0.56 |
| 97_S | 164_N | 1.132 | 0.56 |
| 25_I | 28_E | 1.127 | 0.55 |
| 100_S | 281_V | 1.125 | 0.55 |
| 239_G | 387_L | 1.123 | 0.55 |
| 79_S | 83_N | 1.123 | 0.55 |
| 193_G | 241_A | 1.120 | 0.54 |
| 418_K | 422_E | 1.118 | 0.54 |
| 127_Q | 179_K | 1.116 | 0.54 |
| 144_L | 317_Y | 1.116 | 0.54 |
| 289_D | 293_K | 1.114 | 0.54 |
| 15_N | 454_V | 1.112 | 0.54 |
| 13_V | 20_S | 1.105 | 0.53 |
| 82_V | 85_I | 1.104 | 0.53 |
| 354_D | 473_R | 1.102 | 0.53 |
| 103_F | 285_S | 1.102 | 0.53 |
| 181_A | 184_A | 1.100 | 0.52 |
| 269_G | 273_R | 1.099 | 0.52 |
| 407_L | 414_S | 1.096 | 0.52 |
| 229_F | 467_R | 1.092 | 0.51 |
| 266_D | 269_G | 1.091 | 0.51 |
| 13_V | 18_S | 1.088 | 0.51 |
| 82_V | 86_L | 1.086 | 0.51 |
| 25_I | 42_K | 1.085 | 0.51 |
| 41_A | 407_L | 1.081 | 0.50 |
| 150_Y | 418_K | 1.080 | 0.50 |
| 165_Y | 189_A | 1.076 | 0.50 |
| 28_E | 35_D | 1.076 | 0.50 |
| 33_P | 61_R | 1.075 | 0.50 |
| 298_P | 396_I | 1.075 | 0.50 |
| 387_L | 446_R | 1.073 | 0.50 |
| 247_L | 275_L | 1.069 | 0.49 |
| 28_E | 41_A | 1.067 | 0.49 |
| 236_R | 367_Q | 1.067 | 0.49 |
| 96_S | 429_L | 1.066 | 0.49 |
| 423_R | 427_H | 1.065 | 0.49 |
| 11_T | 16_D | 1.065 | 0.49 |
| 12_G | 18_S | 1.065 | 0.49 |
| 225_R | 311_N | 1.064 | 0.49 |
| 167_F | 177_L | 1.064 | 0.49 |
| 201_G | 223_Y | 1.061 | 0.48 |
| 291_F | 297_S | 1.060 | 0.48 |
| 225_R | 450_R | 1.055 | 0.48 |
| 287_V | 297_S | 1.051 | 0.47 |
| 123_K | 229_F | 1.050 | 0.47 |
| 11_T | 18_S | 1.049 | 0.47 |
| 92_Q | 275_L | 1.046 | 0.47 |
| 271_H | 274_Y | 1.044 | 0.47 |
| 352_R | 359_A | 1.043 | 0.47 |
| 17_A | 145_V | 1.042 | 0.46 |
| 83_N | 87_H | 1.041 | 0.46 |
| 12_G | 15_N | 1.041 | 0.46 |
| 163_A | 280_S | 1.041 | 0.46 |
| 13_V | 17_A | 1.040 | 0.46 |
| 37_G | 45_V | 1.040 | 0.46 |
| 76_K | 89_K | 1.037 | 0.46 |
| 35_D | 268_V | 1.036 | 0.46 |
| 138_K | 181_A | 1.030 | 0.45 |
| 54_A | 187_A | 1.030 | 0.45 |
| 242_L | 271_H | 1.030 | 0.45 |
| 144_L | 414_S | 1.030 | 0.45 |
| 10_S | 19_L | 1.028 | 0.45 |
| 74_I | 78_L | 1.028 | 0.45 |
| 376_P | 380_A | 1.027 | 0.45 |
| 342_S | 362_S | 1.026 | 0.45 |
| 13_V | 16_D | 1.026 | 0.45 |
| 11_T | 14_A | 1.026 | 0.45 |
| 163_A | 229_F | 1.026 | 0.45 |
| 12_G | 119_L | 1.025 | 0.45 |
| 21_L | 26_L | 1.021 | 0.44 |
| 127_Q | 176_L | 1.021 | 0.44 |
| 25_I | 29_A | 1.020 | 0.44 |
| 84_E | 419_S | 1.020 | 0.44 |
| 348_G | 365_S | 1.018 | 0.44 |
| 214_L | 317_Y | 1.018 | 0.44 |
| 83_N | 410_E | 1.017 | 0.44 |
| 150_Y | 354_D | 1.010 | 0.43 |
| 121_A | 165_Y | 1.008 | 0.43 |
| 435_D | 443_V | 1.008 | 0.43 |
| 28_E | 32_K | 1.007 | 0.43 |
| 301_I | 479_M | 1.005 | 0.43 |
| 47_A | 51_E | 1.005 | 0.43 |
| 451_A | 473_R | 1.005 | 0.43 |
| 26_L | 34_K | 1.002 | 0.42 |
| 85_I | 293_K | 1.000 | 0.42 |
| 153_F | 352_R | 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 | |
| 2jxfA | 1 | 0.0445 | 23.3 | 0.985 | Contact Map |
| 3kshA | 1 | 0.2915 | 9.7 | 0.987 | Contact Map |
| 3biaX | 1 | 0.2206 | 8.1 | 0.987 | Contact Map |
| 1ug8A | 1 | 0.1579 | 7.8 | 0.988 | Contact Map |
| 3mmhA | 2 | 0.3239 | 7.4 | 0.988 | Contact Map |
| 3j80H | 1 | 0.1599 | 7.3 | 0.988 | Contact Map |
| 2clyA | 2 | 0.1012 | 7.1 | 0.988 | Contact Map |
| 4mn7A | 2 | 0.2834 | 6.3 | 0.988 | Contact Map |
| 3j7aJ | 1 | 0.164 | 5.8 | 0.988 | Contact Map |
| 2lwfA | 1 | 0.2287 | 5.6 | 0.988 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)