| MSA -06 it 0 |
| ID: | 1489614027 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 424 (374) | ||
| Sequences: | 680 (387.6) | ||
| Seq/Len: | 1.818 | ||
| Nf(neff/√len): | 20.0 |
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: 1.818).
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 |
| 390_C | 393_N | 2.860 | 1.00 |
| 316_N | 319_R | 2.651 | 1.00 |
| 390_C | 395_E | 2.465 | 1.00 |
| 382_G | 390_C | 2.372 | 1.00 |
| 84_T | 90_T | 2.223 | 1.00 |
| 111_C | 117_W | 2.135 | 0.99 |
| 385_V | 393_N | 2.133 | 0.99 |
| 385_V | 395_E | 2.131 | 0.99 |
| 76_D | 80_C | 2.110 | 0.99 |
| 166_L | 184_K | 2.057 | 0.99 |
| 382_G | 393_N | 2.009 | 0.99 |
| 389_F | 395_E | 1.990 | 0.99 |
| 382_G | 395_E | 1.973 | 0.99 |
| 73_R | 83_D | 1.954 | 0.98 |
| 71_C | 80_C | 1.906 | 0.98 |
| 127_W | 133_C | 1.865 | 0.98 |
| 388_I | 393_N | 1.840 | 0.97 |
| 226_Y | 238_E | 1.830 | 0.97 |
| 382_G | 385_V | 1.820 | 0.97 |
| 389_F | 393_N | 1.812 | 0.97 |
| 386_A | 395_E | 1.800 | 0.97 |
| 386_A | 390_C | 1.702 | 0.95 |
| 79_L | 92_Q | 1.699 | 0.95 |
| 370_Y | 375_H | 1.692 | 0.95 |
| 393_N | 396_V | 1.689 | 0.95 |
| 385_V | 390_C | 1.663 | 0.95 |
| 314_L | 339_A | 1.659 | 0.95 |
| 71_C | 81_W | 1.658 | 0.95 |
| 71_C | 76_D | 1.654 | 0.94 |
| 154_G | 162_L | 1.626 | 0.94 |
| 189_S | 231_N | 1.616 | 0.93 |
| 80_C | 95_P | 1.588 | 0.93 |
| 388_I | 395_E | 1.577 | 0.92 |
| 381_Q | 393_N | 1.566 | 0.92 |
| 386_A | 389_F | 1.561 | 0.92 |
| 386_A | 393_N | 1.550 | 0.91 |
| 390_C | 396_V | 1.550 | 0.91 |
| 344_L | 348_P | 1.514 | 0.90 |
| 339_A | 342_A | 1.513 | 0.90 |
| 382_G | 389_F | 1.512 | 0.90 |
| 180_I | 193_N | 1.500 | 0.90 |
| 129_N | 133_C | 1.499 | 0.90 |
| 58_M | 73_R | 1.482 | 0.89 |
| 115_G | 127_W | 1.465 | 0.88 |
| 385_V | 389_F | 1.457 | 0.88 |
| 243_H | 316_N | 1.413 | 0.86 |
| 260_Y | 316_N | 1.411 | 0.85 |
| 154_G | 158_S | 1.397 | 0.85 |
| 370_Y | 374_M | 1.396 | 0.85 |
| 382_G | 396_V | 1.396 | 0.85 |
| 158_S | 162_L | 1.383 | 0.84 |
| 238_E | 242_L | 1.353 | 0.82 |
| 71_C | 95_P | 1.352 | 0.82 |
| 169_F | 271_P | 1.348 | 0.82 |
| 235_M | 314_L | 1.346 | 0.82 |
| 76_D | 81_W | 1.338 | 0.81 |
| 279_R | 285_D | 1.335 | 0.81 |
| 154_G | 168_I | 1.331 | 0.81 |
| 234_W | 238_E | 1.329 | 0.80 |
| 233_F | 263_L | 1.329 | 0.80 |
| 174_S | 314_L | 1.328 | 0.80 |
| 243_H | 248_V | 1.322 | 0.80 |
| 381_Q | 390_C | 1.317 | 0.80 |
| 76_D | 95_P | 1.310 | 0.79 |
| 346_L | 351_G | 1.303 | 0.79 |
| 371_D | 374_M | 1.303 | 0.79 |
| 174_S | 180_I | 1.301 | 0.78 |
| 375_H | 378_M | 1.300 | 0.78 |
| 231_N | 353_Q | 1.297 | 0.78 |
| 80_C | 94_C | 1.294 | 0.78 |
| 243_H | 319_R | 1.294 | 0.78 |
| 180_I | 275_H | 1.287 | 0.77 |
| 240_I | 313_F | 1.282 | 0.77 |
| 399_A | 404_W | 1.272 | 0.76 |
| 297_Y | 301_G | 1.268 | 0.76 |
| 241_Y | 264_G | 1.266 | 0.76 |
| 120_H | 123_S | 1.263 | 0.75 |
| 224_H | 350_L | 1.259 | 0.75 |
| 235_M | 342_A | 1.258 | 0.75 |
| 387_T | 392_F | 1.258 | 0.75 |
| 179_R | 183_H | 1.256 | 0.75 |
| 195_V | 199_A | 1.255 | 0.75 |
| 390_C | 394_G | 1.248 | 0.74 |
| 388_I | 392_F | 1.241 | 0.74 |
| 117_W | 121_P | 1.237 | 0.73 |
| 392_F | 395_E | 1.233 | 0.73 |
| 314_L | 342_A | 1.232 | 0.73 |
| 155_H | 165_S | 1.224 | 0.72 |
| 178_Q | 189_S | 1.219 | 0.72 |
| 299_V | 303_V | 1.211 | 0.71 |
| 383_L | 387_T | 1.209 | 0.71 |
| 238_E | 265_W | 1.197 | 0.70 |
| 161_S | 383_L | 1.197 | 0.70 |
| 184_K | 394_G | 1.192 | 0.69 |
| 148_Y | 151_A | 1.191 | 0.69 |
| 178_Q | 181_T | 1.187 | 0.69 |
| 278_A | 298_I | 1.187 | 0.69 |
| 81_W | 94_C | 1.185 | 0.69 |
| 232_Y | 251_F | 1.173 | 0.68 |
| 249_A | 318_V | 1.168 | 0.67 |
| 342_A | 374_M | 1.166 | 0.67 |
| 402_R | 405_M | 1.162 | 0.66 |
| 240_I | 250_V | 1.159 | 0.66 |
| 385_V | 388_I | 1.158 | 0.66 |
| 257_L | 260_Y | 1.153 | 0.66 |
| 340_V | 347_V | 1.151 | 0.65 |
| 255_Q | 355_V | 1.149 | 0.65 |
| 71_C | 94_C | 1.148 | 0.65 |
| 218_K | 343_T | 1.146 | 0.65 |
| 108_S | 132_L | 1.143 | 0.65 |
| 217_C | 238_E | 1.142 | 0.65 |
| 151_A | 332_E | 1.140 | 0.64 |
| 248_V | 251_F | 1.135 | 0.64 |
| 239_G | 260_Y | 1.127 | 0.63 |
| 53_K | 61_A | 1.123 | 0.63 |
| 154_G | 161_S | 1.123 | 0.63 |
| 238_E | 241_Y | 1.117 | 0.62 |
| 239_G | 242_L | 1.115 | 0.62 |
| 236_L | 245_L | 1.114 | 0.62 |
| 235_M | 339_A | 1.113 | 0.62 |
| 220_L | 252_A | 1.113 | 0.62 |
| 179_R | 187_F | 1.110 | 0.61 |
| 218_K | 284_N | 1.108 | 0.61 |
| 119_R | 127_W | 1.106 | 0.61 |
| 112_D | 116_N | 1.105 | 0.61 |
| 391_F | 395_E | 1.104 | 0.61 |
| 222_F | 276_A | 1.102 | 0.60 |
| 277_V | 281_K | 1.096 | 0.60 |
| 176_S | 180_I | 1.095 | 0.60 |
| 386_A | 394_G | 1.095 | 0.60 |
| 177_C | 190_Y | 1.092 | 0.59 |
| 318_V | 322_V | 1.088 | 0.59 |
| 40_N | 43_I | 1.086 | 0.59 |
| 274_I | 278_A | 1.085 | 0.59 |
| 382_G | 388_I | 1.083 | 0.58 |
| 348_P | 381_Q | 1.080 | 0.58 |
| 235_M | 246_I | 1.077 | 0.58 |
| 165_S | 180_I | 1.077 | 0.58 |
| 185_N | 263_L | 1.076 | 0.58 |
| 189_S | 353_Q | 1.074 | 0.57 |
| 75_W | 78_W | 1.074 | 0.57 |
| 114_T | 273_S | 1.074 | 0.57 |
| 388_I | 391_F | 1.073 | 0.57 |
| 187_F | 194_S | 1.067 | 0.57 |
| 399_A | 402_R | 1.063 | 0.56 |
| 154_G | 164_I | 1.061 | 0.56 |
| 152_I | 201_L | 1.059 | 0.56 |
| 190_Y | 338_K | 1.059 | 0.56 |
| 382_G | 386_A | 1.059 | 0.56 |
| 277_V | 356_I | 1.059 | 0.56 |
| 168_I | 175_L | 1.056 | 0.56 |
| 339_A | 399_A | 1.056 | 0.56 |
| 178_Q | 182_L | 1.053 | 0.55 |
| 268_P | 275_H | 1.052 | 0.55 |
| 217_C | 226_Y | 1.051 | 0.55 |
| 311_F | 319_R | 1.046 | 0.54 |
| 323_T | 345_I | 1.044 | 0.54 |
| 387_T | 402_R | 1.040 | 0.54 |
| 346_L | 381_Q | 1.040 | 0.54 |
| 154_G | 177_C | 1.038 | 0.54 |
| 298_I | 383_L | 1.038 | 0.54 |
| 180_I | 194_S | 1.037 | 0.54 |
| 225_Q | 230_C | 1.035 | 0.53 |
| 231_N | 306_A | 1.035 | 0.53 |
| 226_Y | 234_W | 1.032 | 0.53 |
| 190_Y | 193_N | 1.032 | 0.53 |
| 150_M | 219_V | 1.032 | 0.53 |
| 158_S | 172_F | 1.030 | 0.53 |
| 296_L | 300_H | 1.027 | 0.52 |
| 234_W | 265_W | 1.024 | 0.52 |
| 109_K | 117_W | 1.023 | 0.52 |
| 129_N | 211_V | 1.022 | 0.52 |
| 111_C | 211_V | 1.022 | 0.52 |
| 329_H | 337_M | 1.021 | 0.52 |
| 314_L | 399_A | 1.021 | 0.52 |
| 166_L | 221_Q | 1.020 | 0.52 |
| 342_A | 399_A | 1.015 | 0.51 |
| 128_S | 133_C | 1.015 | 0.51 |
| 195_V | 401_K | 1.013 | 0.51 |
| 152_I | 181_T | 1.013 | 0.51 |
| 235_M | 320_V | 1.012 | 0.51 |
| 169_F | 387_T | 1.008 | 0.50 |
| 117_W | 211_V | 1.006 | 0.50 |
| 277_V | 280_A | 1.005 | 0.50 |
| 53_K | 57_R | 1.002 | 0.50 |
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 | |
| 4k5yA | 3 | 0.592 | 100 | 0.603 | Contact Map |
| 4l6rA | 1 | 0.8821 | 100 | 0.668 | Contact Map |
| 4jkvA | 2 | 0.8561 | 100 | 0.818 | Contact Map |
| 4rwfA | 1 | 0 | 100 | 0.821 | Contact Map |
| 4qinA | 1 | 0.6698 | 99.9 | 0.831 | Contact Map |
| 3c5tA | 1 | 0.2406 | 99.9 | 0.832 | Contact Map |
| 4ersA | 1 | 0.2217 | 99.9 | 0.837 | Contact Map |
| 4hj0A | 2 | 0.2099 | 99.9 | 0.847 | Contact Map |
| 2qkhA | 1 | 0.217 | 99.9 | 0.847 | Contact Map |
| 1u34A | 1 | 0.2642 | 99.9 | 0.852 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)