| t6ss |
| ID: | 1432884652 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 494 (485) | ||
| Sequences: | 676 (352.9) | ||
| Seq/Len: | 1.394 | ||
| Nf(neff/√len): | 16.0 |
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: 1.394).
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 | 5.143 | 1.00 |
| 229_F | 238_V | 4.816 | 1.00 |
| 162_S | 284_T | 4.462 | 1.00 |
| 247_L | 277_G | 3.668 | 1.00 |
| 274_Y | 315_H | 3.204 | 1.00 |
| 164_N | 281_V | 2.647 | 1.00 |
| 163_A | 191_F | 2.535 | 1.00 |
| 238_V | 366_T | 2.440 | 1.00 |
| 160_I | 287_V | 2.385 | 1.00 |
| 253_E | 264_T | 2.364 | 0.99 |
| 73_E | 76_K | 2.243 | 0.99 |
| 192_I | 283_L | 2.240 | 0.99 |
| 239_G | 365_S | 2.207 | 0.99 |
| 228_S | 356_D | 2.173 | 0.99 |
| 102_K | 106_D | 2.156 | 0.99 |
| 231_E | 368_K | 2.150 | 0.99 |
| 141_L | 180_C | 2.131 | 0.99 |
| 229_F | 366_T | 2.120 | 0.99 |
| 188_H | 237_Y | 2.116 | 0.99 |
| 271_H | 326_K | 2.054 | 0.98 |
| 241_A | 279_A | 2.035 | 0.98 |
| 314_L | 325_T | 2.032 | 0.98 |
| 122_S | 125_D | 1.986 | 0.98 |
| 120_N | 125_D | 1.892 | 0.96 |
| 171_P | 255_T | 1.861 | 0.96 |
| 199_V | 346_F | 1.853 | 0.96 |
| 51_E | 54_A | 1.844 | 0.96 |
| 244_R | 330_E | 1.811 | 0.95 |
| 252_G | 255_T | 1.763 | 0.94 |
| 96_S | 275_L | 1.751 | 0.94 |
| 299_N | 441_P | 1.742 | 0.94 |
| 239_G | 347_I | 1.731 | 0.93 |
| 147_S | 334_T | 1.697 | 0.92 |
| 171_P | 249_L | 1.690 | 0.92 |
| 20_S | 23_D | 1.688 | 0.92 |
| 151_G | 334_T | 1.669 | 0.92 |
| 308_A | 355_S | 1.647 | 0.91 |
| 339_F | 343_E | 1.629 | 0.90 |
| 417_E | 420_D | 1.618 | 0.90 |
| 125_D | 180_C | 1.604 | 0.89 |
| 117_E | 158_Y | 1.599 | 0.89 |
| 103_F | 107_R | 1.592 | 0.89 |
| 23_D | 42_K | 1.584 | 0.89 |
| 150_Y | 237_Y | 1.576 | 0.88 |
| 115_R | 156_K | 1.572 | 0.88 |
| 429_L | 454_V | 1.564 | 0.88 |
| 390_Q | 479_M | 1.564 | 0.88 |
| 422_E | 426_N | 1.554 | 0.87 |
| 417_E | 473_R | 1.553 | 0.87 |
| 167_F | 176_L | 1.538 | 0.87 |
| 437_D | 450_R | 1.535 | 0.86 |
| 236_R | 388_G | 1.530 | 0.86 |
| 270_H | 273_R | 1.526 | 0.86 |
| 195_A | 199_V | 1.515 | 0.85 |
| 142_Y | 410_E | 1.512 | 0.85 |
| 245_F | 277_G | 1.507 | 0.85 |
| 286_R | 289_D | 1.483 | 0.84 |
| 434_S | 439_P | 1.481 | 0.84 |
| 147_S | 151_G | 1.461 | 0.83 |
| 131_E | 175_E | 1.459 | 0.82 |
| 144_L | 148_N | 1.430 | 0.81 |
| 96_S | 277_G | 1.412 | 0.79 |
| 363_A | 392_P | 1.391 | 0.78 |
| 112_E | 215_K | 1.386 | 0.78 |
| 200_F | 346_F | 1.384 | 0.78 |
| 215_K | 344_E | 1.377 | 0.77 |
| 271_H | 315_H | 1.362 | 0.76 |
| 78_L | 82_V | 1.361 | 0.76 |
| 80_S | 263_F | 1.341 | 0.74 |
| 29_A | 51_E | 1.338 | 0.74 |
| 89_K | 272_E | 1.335 | 0.74 |
| 233_E | 466_Y | 1.334 | 0.74 |
| 80_S | 84_E | 1.320 | 0.73 |
| 342_S | 365_S | 1.318 | 0.73 |
| 128_K | 259_K | 1.314 | 0.72 |
| 150_Y | 491_L | 1.314 | 0.72 |
| 15_N | 18_S | 1.302 | 0.71 |
| 109_D | 292_A | 1.301 | 0.71 |
| 82_V | 446_R | 1.284 | 0.70 |
| 369_P | 389_T | 1.284 | 0.70 |
| 187_A | 273_R | 1.283 | 0.70 |
| 240_L | 412_I | 1.283 | 0.70 |
| 172_Q | 256_V | 1.278 | 0.69 |
| 152_V | 334_T | 1.272 | 0.69 |
| 76_K | 80_S | 1.267 | 0.68 |
| 153_F | 188_H | 1.265 | 0.68 |
| 404_I | 470_L | 1.261 | 0.68 |
| 242_L | 348_G | 1.261 | 0.68 |
| 187_A | 197_P | 1.257 | 0.67 |
| 14_A | 17_A | 1.250 | 0.67 |
| 335_E | 436_M | 1.249 | 0.67 |
| 372_F | 385_Y | 1.247 | 0.66 |
| 10_S | 14_A | 1.246 | 0.66 |
| 279_A | 398_T | 1.242 | 0.66 |
| 337_R | 340_E | 1.235 | 0.65 |
| 348_G | 404_I | 1.233 | 0.65 |
| 342_S | 363_A | 1.232 | 0.65 |
| 245_F | 282_A | 1.232 | 0.65 |
| 185_A | 234_D | 1.230 | 0.65 |
| 135_E | 225_R | 1.226 | 0.65 |
| 150_Y | 257_P | 1.222 | 0.64 |
| 465_W | 480_G | 1.208 | 0.63 |
| 11_T | 16_D | 1.207 | 0.63 |
| 420_D | 473_R | 1.204 | 0.62 |
| 479_M | 483_F | 1.201 | 0.62 |
| 223_Y | 485_L | 1.199 | 0.62 |
| 301_I | 477_K | 1.198 | 0.62 |
| 172_Q | 257_P | 1.194 | 0.61 |
| 163_A | 223_Y | 1.194 | 0.61 |
| 400_L | 472_V | 1.193 | 0.61 |
| 179_K | 182_S | 1.185 | 0.61 |
| 205_F | 472_V | 1.184 | 0.61 |
| 41_A | 407_L | 1.175 | 0.60 |
| 12_G | 16_D | 1.175 | 0.60 |
| 71_I | 74_I | 1.173 | 0.59 |
| 303_P | 359_A | 1.172 | 0.59 |
| 145_V | 158_Y | 1.172 | 0.59 |
| 162_S | 287_V | 1.170 | 0.59 |
| 379_K | 382_E | 1.168 | 0.59 |
| 194_N | 241_A | 1.164 | 0.59 |
| 117_E | 454_V | 1.163 | 0.58 |
| 290_S | 418_K | 1.158 | 0.58 |
| 435_D | 439_P | 1.156 | 0.58 |
| 161_I | 184_A | 1.156 | 0.58 |
| 100_S | 247_L | 1.149 | 0.57 |
| 266_D | 273_R | 1.143 | 0.56 |
| 181_A | 184_A | 1.143 | 0.56 |
| 475_H | 491_L | 1.141 | 0.56 |
| 147_S | 411_Q | 1.141 | 0.56 |
| 104_M | 285_S | 1.140 | 0.56 |
| 239_G | 387_L | 1.135 | 0.56 |
| 10_S | 13_V | 1.132 | 0.55 |
| 79_S | 83_N | 1.128 | 0.55 |
| 28_E | 31_L | 1.120 | 0.54 |
| 100_S | 281_V | 1.119 | 0.54 |
| 289_D | 293_K | 1.113 | 0.53 |
| 25_I | 29_A | 1.110 | 0.53 |
| 144_L | 317_Y | 1.109 | 0.53 |
| 25_I | 28_E | 1.107 | 0.53 |
| 11_T | 15_N | 1.106 | 0.53 |
| 127_Q | 179_K | 1.104 | 0.53 |
| 269_G | 273_R | 1.101 | 0.52 |
| 165_Y | 189_A | 1.100 | 0.52 |
| 25_I | 42_K | 1.099 | 0.52 |
| 103_F | 285_S | 1.095 | 0.52 |
| 82_V | 85_I | 1.095 | 0.52 |
| 354_D | 473_R | 1.093 | 0.51 |
| 266_D | 269_G | 1.093 | 0.51 |
| 96_S | 429_L | 1.091 | 0.51 |
| 26_L | 34_K | 1.090 | 0.51 |
| 229_F | 467_R | 1.090 | 0.51 |
| 15_N | 454_V | 1.088 | 0.51 |
| 150_Y | 418_K | 1.087 | 0.51 |
| 418_K | 422_E | 1.087 | 0.51 |
| 11_T | 18_S | 1.086 | 0.51 |
| 13_V | 20_S | 1.084 | 0.51 |
| 298_P | 396_I | 1.081 | 0.50 |
| 387_L | 446_R | 1.078 | 0.50 |
| 82_V | 86_L | 1.078 | 0.50 |
| 17_A | 145_V | 1.076 | 0.50 |
| 407_L | 414_S | 1.076 | 0.50 |
| 37_G | 45_V | 1.073 | 0.49 |
| 225_R | 311_N | 1.072 | 0.49 |
| 236_R | 367_Q | 1.072 | 0.49 |
| 225_R | 450_R | 1.068 | 0.49 |
| 10_S | 19_L | 1.067 | 0.49 |
| 193_G | 241_A | 1.066 | 0.49 |
| 247_L | 275_L | 1.066 | 0.49 |
| 54_A | 187_A | 1.064 | 0.49 |
| 97_S | 164_N | 1.063 | 0.48 |
| 423_R | 427_H | 1.061 | 0.48 |
| 76_K | 89_K | 1.060 | 0.48 |
| 167_F | 177_L | 1.060 | 0.48 |
| 48_F | 454_V | 1.059 | 0.48 |
| 13_V | 17_A | 1.059 | 0.48 |
| 28_E | 41_A | 1.058 | 0.48 |
| 36_E | 40_V | 1.058 | 0.48 |
| 163_A | 280_S | 1.057 | 0.48 |
| 21_L | 26_L | 1.052 | 0.47 |
| 352_R | 359_A | 1.050 | 0.47 |
| 123_K | 229_F | 1.050 | 0.47 |
| 144_L | 414_S | 1.049 | 0.47 |
| 13_V | 18_S | 1.048 | 0.47 |
| 92_Q | 275_L | 1.048 | 0.47 |
| 83_N | 87_H | 1.047 | 0.47 |
| 271_H | 274_Y | 1.047 | 0.47 |
| 287_V | 297_S | 1.044 | 0.46 |
| 12_G | 15_N | 1.043 | 0.46 |
| 12_G | 18_S | 1.041 | 0.46 |
| 435_D | 443_V | 1.039 | 0.46 |
| 201_G | 223_Y | 1.035 | 0.46 |
| 376_P | 380_A | 1.033 | 0.45 |
| 29_A | 32_K | 1.032 | 0.45 |
| 121_A | 165_Y | 1.031 | 0.45 |
| 214_L | 317_Y | 1.031 | 0.45 |
| 11_T | 14_A | 1.030 | 0.45 |
| 74_I | 78_L | 1.029 | 0.45 |
| 242_L | 271_H | 1.027 | 0.45 |
| 85_I | 293_K | 1.025 | 0.45 |
| 84_E | 419_S | 1.023 | 0.44 |
| 28_E | 35_D | 1.022 | 0.44 |
| 83_N | 410_E | 1.020 | 0.44 |
| 291_F | 297_S | 1.020 | 0.44 |
| 342_S | 362_S | 1.020 | 0.44 |
| 138_K | 181_A | 1.019 | 0.44 |
| 145_V | 206_L | 1.018 | 0.44 |
| 127_Q | 176_L | 1.018 | 0.44 |
| 348_G | 365_S | 1.014 | 0.43 |
| 301_I | 479_M | 1.007 | 0.43 |
| 96_S | 247_L | 1.007 | 0.43 |
| 419_S | 422_E | 1.003 | 0.42 |
| 297_S | 395_F | 1.002 | 0.42 |
| 150_Y | 354_D | 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 | 21.3 | 0.985 | Contact Map |
| 1ug8A | 1 | 0.1559 | 9.4 | 0.987 | Contact Map |
| 3j80H | 1 | 0.1599 | 8.7 | 0.987 | Contact Map |
| 3kshA | 1 | 0.2915 | 7.8 | 0.988 | Contact Map |
| 3biaX | 1 | 0.2206 | 6.9 | 0.988 | Contact Map |
| 3mmhA | 2 | 0.3239 | 6.8 | 0.988 | Contact Map |
| 1ujlA | 1 | 0.0688 | 6.6 | 0.988 | Contact Map |
| 2clyA | 2 | 0.1012 | 6.5 | 0.988 | Contact Map |
| 4mn7A | 2 | 0.2834 | 6.1 | 0.988 | Contact Map |
| 3j7aJ | 1 | 0.164 | 6 | 0.988 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)