| crf v5 |
| ID: | 1490633261 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 407 (342) | ||
| Sequences: | 660 (353.4) | ||
| Seq/Len: | 1.930 | ||
| Nf(neff/√len): | 19.1 |
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: 1.930).
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 |
| 393_C | 396_N | 3.407 | 1.00 |
| 393_C | 398_E | 2.892 | 1.00 |
| 318_N | 321_R | 2.840 | 1.00 |
| 88_S | 94_V | 2.455 | 1.00 |
| 392_Y | 398_E | 2.422 | 1.00 |
| 396_N | 399_S | 2.391 | 1.00 |
| 392_Y | 396_N | 2.286 | 1.00 |
| 74_C | 84_C | 2.262 | 1.00 |
| 74_C | 85_W | 2.256 | 1.00 |
| 79_D | 84_C | 2.192 | 1.00 |
| 74_C | 79_D | 2.144 | 0.99 |
| 76_T | 87_R | 2.091 | 0.99 |
| 393_C | 399_S | 2.079 | 0.99 |
| 394_F | 398_E | 2.066 | 0.99 |
| 168_F | 186_W | 2.037 | 0.99 |
| 226_Y | 238_E | 1.849 | 0.98 |
| 83_T | 96_R | 1.798 | 0.97 |
| 316_L | 341_A | 1.716 | 0.96 |
| 79_D | 85_W | 1.674 | 0.95 |
| 395_F | 398_E | 1.663 | 0.95 |
| 344_A | 377_N | 1.633 | 0.95 |
| 163_A | 386_F | 1.631 | 0.94 |
| 156_G | 170_L | 1.613 | 0.94 |
| 278_G | 300_I | 1.609 | 0.94 |
| 156_G | 164_L | 1.559 | 0.93 |
| 180_L | 191_T | 1.543 | 0.92 |
| 233_F | 263_I | 1.541 | 0.92 |
| 393_C | 397_G | 1.517 | 0.91 |
| 243_H | 321_R | 1.514 | 0.91 |
| 85_W | 98_C | 1.509 | 0.91 |
| 84_C | 98_C | 1.504 | 0.91 |
| 243_H | 318_N | 1.502 | 0.91 |
| 191_T | 231_N | 1.498 | 0.90 |
| 299_Y | 303_G | 1.472 | 0.89 |
| 84_C | 99_P | 1.456 | 0.89 |
| 238_E | 265_W | 1.433 | 0.88 |
| 238_E | 242_L | 1.427 | 0.87 |
| 74_C | 99_P | 1.424 | 0.87 |
| 394_F | 399_S | 1.421 | 0.87 |
| 341_A | 344_A | 1.411 | 0.87 |
| 268_P | 275_W | 1.392 | 0.86 |
| 74_C | 98_C | 1.382 | 0.85 |
| 235_M | 316_L | 1.381 | 0.85 |
| 385_G | 396_N | 1.378 | 0.85 |
| 231_N | 355_T | 1.357 | 0.84 |
| 385_G | 393_C | 1.350 | 0.83 |
| 224_F | 352_L | 1.336 | 0.82 |
| 74_C | 78_L | 1.327 | 0.82 |
| 156_G | 160_S | 1.325 | 0.82 |
| 171_F | 309_L | 1.322 | 0.81 |
| 388_V | 396_N | 1.315 | 0.81 |
| 182_N | 195_R | 1.309 | 0.80 |
| 240_C | 315_F | 1.307 | 0.80 |
| 232_F | 337_Q | 1.305 | 0.80 |
| 402_K | 407_W | 1.298 | 0.80 |
| 301_Y | 305_I | 1.294 | 0.79 |
| 392_Y | 399_S | 1.292 | 0.79 |
| 157_H | 167_A | 1.291 | 0.79 |
| 379_F | 387_F | 1.289 | 0.79 |
| 277_I | 281_Y | 1.289 | 0.79 |
| 346_L | 350_P | 1.282 | 0.79 |
| 260_F | 318_N | 1.275 | 0.78 |
| 182_N | 275_W | 1.273 | 0.78 |
| 160_S | 164_L | 1.271 | 0.78 |
| 392_Y | 395_F | 1.267 | 0.77 |
| 389_S | 393_C | 1.267 | 0.77 |
| 239_G | 260_F | 1.257 | 0.77 |
| 279_K | 285_E | 1.257 | 0.77 |
| 234_W | 238_E | 1.249 | 0.76 |
| 324_M | 328_R | 1.246 | 0.76 |
| 320_V | 324_M | 1.239 | 0.75 |
| 197_V | 201_L | 1.239 | 0.75 |
| 180_L | 183_V | 1.237 | 0.75 |
| 316_L | 344_A | 1.233 | 0.75 |
| 79_D | 98_C | 1.231 | 0.74 |
| 218_R | 284_N | 1.229 | 0.74 |
| 171_F | 271_I | 1.217 | 0.73 |
| 342_V | 349_L | 1.213 | 0.73 |
| 235_M | 344_A | 1.213 | 0.73 |
| 243_H | 248_M | 1.197 | 0.72 |
| 390_V | 395_F | 1.196 | 0.71 |
| 114_Y | 131_Q | 1.195 | 0.71 |
| 217_C | 238_E | 1.193 | 0.71 |
| 71_Y | 75_N | 1.192 | 0.71 |
| 162_A | 276_A | 1.185 | 0.70 |
| 348_L | 353_G | 1.185 | 0.70 |
| 218_R | 345_T | 1.180 | 0.70 |
| 165_V | 277_I | 1.180 | 0.70 |
| 388_V | 398_E | 1.176 | 0.70 |
| 238_E | 241_Y | 1.168 | 0.69 |
| 231_N | 265_W | 1.167 | 0.69 |
| 78_L | 81_I | 1.162 | 0.68 |
| 176_S | 182_N | 1.157 | 0.68 |
| 235_M | 341_A | 1.154 | 0.68 |
| 201_L | 270_P | 1.154 | 0.68 |
| 185_H | 188_L | 1.153 | 0.67 |
| 257_K | 260_F | 1.145 | 0.67 |
| 385_G | 398_E | 1.143 | 0.66 |
| 385_G | 388_V | 1.136 | 0.66 |
| 156_G | 163_A | 1.127 | 0.65 |
| 171_F | 390_V | 1.126 | 0.65 |
| 85_W | 99_P | 1.122 | 0.64 |
| 72_S | 88_S | 1.121 | 0.64 |
| 240_C | 250_Y | 1.120 | 0.64 |
| 152_V | 379_F | 1.119 | 0.64 |
| 239_G | 323_L | 1.116 | 0.64 |
| 392_Y | 397_G | 1.112 | 0.63 |
| 180_L | 184_I | 1.110 | 0.63 |
| 123_W | 126_R | 1.106 | 0.63 |
| 79_D | 99_P | 1.104 | 0.62 |
| 186_W | 397_G | 1.099 | 0.62 |
| 189_I | 196_N | 1.099 | 0.62 |
| 226_Y | 234_W | 1.099 | 0.62 |
| 389_S | 398_E | 1.097 | 0.62 |
| 178_R | 182_N | 1.091 | 0.61 |
| 262_F | 323_L | 1.090 | 0.61 |
| 358_L | 376_F | 1.087 | 0.61 |
| 166_A | 190_T | 1.085 | 0.60 |
| 167_A | 182_N | 1.083 | 0.60 |
| 160_S | 167_A | 1.082 | 0.60 |
| 127_I | 131_Q | 1.079 | 0.60 |
| 177_I | 226_Y | 1.078 | 0.60 |
| 327_L | 389_S | 1.078 | 0.60 |
| 176_S | 316_L | 1.078 | 0.60 |
| 95_E | 114_Y | 1.069 | 0.59 |
| 241_Y | 264_G | 1.069 | 0.59 |
| 350_P | 384_Q | 1.065 | 0.58 |
| 226_Y | 265_W | 1.064 | 0.58 |
| 226_Y | 319_I | 1.060 | 0.58 |
| 128_N | 132_C | 1.057 | 0.57 |
| 121_G | 132_C | 1.052 | 0.57 |
| 313_F | 321_R | 1.049 | 0.57 |
| 230_T | 260_F | 1.047 | 0.56 |
| 391_F | 394_F | 1.046 | 0.56 |
| 231_N | 308_V | 1.044 | 0.56 |
| 237_V | 275_W | 1.040 | 0.56 |
| 117_C | 132_C | 1.037 | 0.55 |
| 242_L | 265_W | 1.036 | 0.55 |
| 179_C | 192_F | 1.036 | 0.55 |
| 334_E | 338_Y | 1.035 | 0.55 |
| 195_R | 275_W | 1.035 | 0.55 |
| 116_E | 354_I | 1.034 | 0.55 |
| 78_L | 84_C | 1.034 | 0.55 |
| 402_K | 405_H | 1.031 | 0.55 |
| 245_A | 388_V | 1.031 | 0.55 |
| 288_W | 304_P | 1.031 | 0.55 |
| 237_V | 263_I | 1.028 | 0.54 |
| 277_I | 280_L | 1.027 | 0.54 |
| 153_N | 157_H | 1.024 | 0.54 |
| 386_F | 390_V | 1.022 | 0.54 |
| 316_L | 402_K | 1.019 | 0.53 |
| 254_R | 257_K | 1.019 | 0.53 |
| 341_A | 373_F | 1.019 | 0.53 |
| 300_I | 386_F | 1.016 | 0.53 |
| 400_R | 407_W | 1.015 | 0.53 |
| 151_V | 372_V | 1.014 | 0.53 |
| 200_F | 344_A | 1.013 | 0.53 |
| 255_L | 357_M | 1.009 | 0.52 |
| 187_N | 239_G | 1.007 | 0.52 |
| 312_N | 326_K | 1.006 | 0.52 |
| 115_R | 339_R | 1.003 | 0.52 |
| 185_H | 242_L | 1.000 | 0.51 |
| 201_L | 307_L | 1.000 | 0.51 |
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 | 0.6216 | 100 | 0.551 | Contact Map |
| 4l6rA | 1 | 0.8845 | 100 | 0.65 | Contact Map |
| 4jkvA | 2 | 0.8722 | 100 | 0.8 | Contact Map |
| 4qinA | 1 | 0.7027 | 100 | 0.812 | Contact Map |
| 2qkhA | 1 | 0.231 | 99.9 | 0.814 | Contact Map |
| 4hj0A | 2 | 0.226 | 99.9 | 0.824 | Contact Map |
| 1u34A | 1 | 0.2924 | 99.9 | 0.826 | Contact Map |
| 3c5tA | 1 | 0.2383 | 99.9 | 0.827 | Contact Map |
| 4ersA | 1 | 0.2211 | 99.9 | 0.833 | Contact Map |
| 4rwfA | 1 | 0 | 99.9 | 0.833 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)