| spc105 |
| ID: | 1489328471 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 497 (335) | ||
| Sequences: | 6344 (5789.4) | ||
| Seq/Len: | 18.937 | ||
| Nf(neff/√len): | 316.3 |
Jackhmmer Results: (2016_04)
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: 18.937).
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 |
| 241_L | 244_H | 2.798 | 1.00 |
| 213_I | 216_L | 2.782 | 1.00 |
| 272_I | 275_L | 2.515 | 1.00 |
| 279_V | 282_I | 2.465 | 1.00 |
| 227_T | 230_N | 2.394 | 1.00 |
| 314_R | 318_F | 2.278 | 1.00 |
| 234_I | 237_F | 2.275 | 1.00 |
| 192_V | 195_V | 2.262 | 1.00 |
| 248_L | 251_S | 2.257 | 1.00 |
| 265_I | 268_K | 2.220 | 1.00 |
| 185_Y | 188_L | 2.215 | 1.00 |
| 199_R | 202_I | 2.196 | 1.00 |
| 278_E | 283_D | 2.165 | 1.00 |
| 206_N | 209_I | 2.070 | 1.00 |
| 171_E | 174_L | 2.003 | 1.00 |
| 258_M | 261_L | 1.964 | 1.00 |
| 304_L | 307_L | 1.951 | 1.00 |
| 164_K | 167_L | 1.840 | 1.00 |
| 311_T | 314_R | 1.797 | 1.00 |
| 297_L | 300_L | 1.783 | 1.00 |
| 286_I | 289_R | 1.762 | 1.00 |
| 157_M | 160_Y | 1.711 | 1.00 |
| 103_I | 106_S | 1.656 | 1.00 |
| 163_R | 168_N | 1.654 | 1.00 |
| 220_P | 223_S | 1.653 | 1.00 |
| 233_K | 238_K | 1.632 | 1.00 |
| 303_T | 306_I | 1.628 | 1.00 |
| 296_D | 301_R | 1.626 | 1.00 |
| 247_S | 250_S | 1.602 | 1.00 |
| 264_A | 269_S | 1.571 | 1.00 |
| 272_I | 276_R | 1.553 | 1.00 |
| 171_E | 175_A | 1.549 | 1.00 |
| 271_D | 276_R | 1.544 | 1.00 |
| 178_L | 181_L | 1.543 | 1.00 |
| 281_S | 285_K | 1.542 | 1.00 |
| 96_C | 99_L | 1.541 | 1.00 |
| 236_A | 240_E | 1.524 | 1.00 |
| 303_T | 308_E | 1.500 | 1.00 |
| 268_K | 272_I | 1.487 | 1.00 |
| 110_F | 113_F | 1.483 | 1.00 |
| 215_S | 219_L | 1.451 | 1.00 |
| 271_D | 274_T | 1.437 | 1.00 |
| 317_K | 320_K | 1.436 | 1.00 |
| 240_E | 243_E | 1.436 | 1.00 |
| 178_L | 182_K | 1.434 | 1.00 |
| 206_N | 210_K | 1.414 | 1.00 |
| 177_N | 182_K | 1.398 | 0.99 |
| 230_N | 234_I | 1.397 | 0.99 |
| 180_T | 184_E | 1.396 | 0.99 |
| 137_K | 141_R | 1.391 | 0.99 |
| 208_A | 212_E | 1.384 | 0.99 |
| 212_E | 217_K | 1.381 | 0.99 |
| 198_I | 203_R | 1.370 | 0.99 |
| 207_E | 210_K | 1.363 | 0.99 |
| 311_T | 315_F | 1.333 | 0.99 |
| 199_R | 203_R | 1.331 | 0.99 |
| 200_G | 203_R | 1.327 | 0.99 |
| 185_Y | 189_N | 1.319 | 0.99 |
| 205_L | 208_A | 1.313 | 0.99 |
| 115_A | 119_K | 1.304 | 0.99 |
| 210_K | 214_R | 1.290 | 0.99 |
| 184_E | 189_N | 1.290 | 0.99 |
| 367_T | 370_L | 1.287 | 0.99 |
| 194_K | 198_I | 1.281 | 0.99 |
| 192_V | 196_N | 1.273 | 0.99 |
| 216_L | 220_P | 1.272 | 0.99 |
| 195_V | 199_R | 1.270 | 0.99 |
| 157_M | 161_E | 1.268 | 0.99 |
| 359_D | 363_Y | 1.255 | 0.99 |
| 202_I | 206_N | 1.254 | 0.99 |
| 240_E | 245_S | 1.250 | 0.99 |
| 242_M | 246_I | 1.249 | 0.99 |
| 243_E | 247_S | 1.248 | 0.99 |
| 136_M | 141_R | 1.248 | 0.99 |
| 296_D | 299_K | 1.246 | 0.98 |
| 308_E | 312_G | 1.238 | 0.98 |
| 264_A | 267_K | 1.236 | 0.98 |
| 205_L | 210_K | 1.229 | 0.98 |
| 158_E | 162_W | 1.222 | 0.98 |
| 204_K | 208_A | 1.221 | 0.98 |
| 325_I | 328_L | 1.212 | 0.98 |
| 284_K | 288_K | 1.206 | 0.98 |
| 188_L | 192_V | 1.204 | 0.98 |
| 218_N | 222_D | 1.192 | 0.98 |
| 283_D | 287_E | 1.191 | 0.98 |
| 276_R | 280_A | 1.190 | 0.98 |
| 268_K | 271_D | 1.190 | 0.98 |
| 258_M | 262_K | 1.188 | 0.98 |
| 117_I | 120_S | 1.187 | 0.98 |
| 285_K | 290_K | 1.186 | 0.98 |
| 274_T | 278_E | 1.182 | 0.98 |
| 298_P | 302_D | 1.177 | 0.98 |
| 102_S | 107_K | 1.172 | 0.98 |
| 212_E | 215_S | 1.170 | 0.97 |
| 138_Q | 142_D | 1.168 | 0.97 |
| 176_E | 180_T | 1.160 | 0.97 |
| 267_K | 271_D | 1.159 | 0.97 |
| 135_K | 139_L | 1.159 | 0.97 |
| 114_E | 118_D | 1.158 | 0.97 |
| 169_G | 173_I | 1.155 | 0.97 |
| 314_R | 317_K | 1.150 | 0.97 |
| 260_S | 264_A | 1.149 | 0.97 |
| 223_S | 227_T | 1.144 | 0.97 |
| 364_H | 367_T | 1.139 | 0.97 |
| 239_Q | 243_E | 1.139 | 0.97 |
| 233_K | 236_A | 1.138 | 0.97 |
| 306_I | 310_L | 1.137 | 0.97 |
| 247_S | 252_N | 1.136 | 0.97 |
| 241_L | 245_S | 1.134 | 0.97 |
| 318_F | 321_A | 1.133 | 0.97 |
| 316_L | 320_K | 1.132 | 0.97 |
| 95_R | 100_W | 1.132 | 0.97 |
| 322_T | 326_A | 1.129 | 0.97 |
| 213_I | 217_K | 1.129 | 0.97 |
| 109_K | 114_E | 1.126 | 0.97 |
| 314_R | 319_S | 1.123 | 0.97 |
| 158_E | 161_E | 1.122 | 0.97 |
| 173_I | 177_N | 1.117 | 0.96 |
| 143_Q | 146_L | 1.112 | 0.96 |
| 105_E | 109_K | 1.111 | 0.96 |
| 322_T | 327_F | 1.108 | 0.96 |
| 240_E | 244_H | 1.107 | 0.96 |
| 348_S | 367_T | 1.101 | 0.96 |
| 286_I | 290_K | 1.098 | 0.96 |
| 190_E | 194_K | 1.096 | 0.96 |
| 168_N | 172_L | 1.094 | 0.96 |
| 184_E | 187_K | 1.092 | 0.96 |
| 316_L | 319_S | 1.092 | 0.96 |
| 244_H | 248_L | 1.091 | 0.96 |
| 98_E | 102_S | 1.088 | 0.96 |
| 211_E | 215_S | 1.087 | 0.96 |
| 363_Y | 367_T | 1.086 | 0.96 |
| 231_R | 235_E | 1.084 | 0.96 |
| 278_E | 281_S | 1.084 | 0.96 |
| 226_P | 229_M | 1.083 | 0.96 |
| 315_F | 319_S | 1.081 | 0.95 |
| 299_K | 303_T | 1.081 | 0.95 |
| 163_R | 166_Q | 1.077 | 0.95 |
| 162_W | 166_Q | 1.076 | 0.95 |
| 256_Q | 260_S | 1.076 | 0.95 |
| 213_I | 220_P | 1.073 | 0.95 |
| 310_L | 314_R | 1.073 | 0.95 |
| 182_K | 186_E | 1.069 | 0.95 |
| 245_S | 249_S | 1.065 | 0.95 |
| 177_N | 180_T | 1.063 | 0.95 |
| 280_A | 283_D | 1.063 | 0.95 |
| 141_R | 145_Q | 1.062 | 0.95 |
| 287_E | 290_K | 1.058 | 0.95 |
| 369_L | 372_N | 1.058 | 0.95 |
| 275_L | 279_V | 1.057 | 0.95 |
| 201_K | 205_L | 1.056 | 0.95 |
| 222_D | 226_P | 1.054 | 0.95 |
| 225_K | 228_L | 1.053 | 0.95 |
| 118_D | 122_P | 1.053 | 0.95 |
| 367_T | 372_N | 1.052 | 0.95 |
| 298_P | 301_R | 1.049 | 0.94 |
| 366_F | 370_L | 1.046 | 0.94 |
| 323_L | 327_F | 1.045 | 0.94 |
| 262_K | 266_A | 1.044 | 0.94 |
| 102_S | 105_E | 1.044 | 0.94 |
| 302_D | 306_I | 1.044 | 0.94 |
| 261_L | 264_A | 1.040 | 0.94 |
| 207_E | 211_E | 1.039 | 0.94 |
| 242_M | 245_S | 1.038 | 0.94 |
| 363_Y | 366_F | 1.036 | 0.94 |
| 356_S | 360_D | 1.035 | 0.94 |
| 167_L | 171_E | 1.035 | 0.94 |
| 89_L | 92_E | 1.034 | 0.94 |
| 295_F | 299_K | 1.034 | 0.94 |
| 156_A | 161_E | 1.033 | 0.94 |
| 300_L | 304_L | 1.030 | 0.94 |
| 209_I | 213_I | 1.025 | 0.93 |
| 263_L | 267_K | 1.021 | 0.93 |
| 277_S | 280_A | 1.019 | 0.93 |
| 235_E | 238_K | 1.012 | 0.93 |
| 324_S | 328_L | 1.011 | 0.93 |
| 301_R | 305_K | 1.009 | 0.93 |
| 167_L | 170_L | 1.008 | 0.93 |
| 257_E | 260_S | 1.005 | 0.93 |
| 174_L | 178_L | 1.004 | 0.93 |
| 366_F | 372_N | 1.001 | 0.92 |
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 | |
| 4etpA | 1 | 0.4366 | 100 | 0.567 | Contact Map |
| 3u06A | 2 | 0.4406 | 100 | 0.57 | Contact Map |
| 4etpB | 1 | 0.3742 | 100 | 0.585 | Contact Map |
| 3bfnA | 1 | 0.3058 | 99.9 | 0.633 | Contact Map |
| 3t0qA | 1 | 0.3139 | 99.9 | 0.638 | Contact Map |
| 2h58A | 1 | 0.3199 | 99.9 | 0.638 | Contact Map |
| 1f9vA | 1 | 0.3179 | 99.9 | 0.639 | Contact Map |
| 2repA | 1 | 0.3099 | 99.9 | 0.639 | Contact Map |
| 3cobA | 2 | 0.336 | 99.9 | 0.639 | Contact Map |
| 1bg2A | 1 | 0.3421 | 99.9 | 0.647 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)