| student |
| ID: | 1504547517 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 407 (395) | ||
| Sequences: | 570 (384.3) | ||
| Seq/Len: | 1.443 | ||
| Nf(neff/√len): | 19.3 |
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: 1.443).
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 |
| 394_Q | 405_G | 3.162 | 1.00 |
| 113_S | 151_E | 2.976 | 1.00 |
| 357_K | 366_T | 2.975 | 1.00 |
| 44_L | 280_Y | 2.775 | 1.00 |
| 99_N | 107_M | 2.754 | 1.00 |
| 391_Q | 394_Q | 2.454 | 1.00 |
| 273_E | 288_F | 2.304 | 0.99 |
| 144_Y | 347_D | 2.274 | 0.99 |
| 390_H | 394_Q | 2.238 | 0.99 |
| 18_D | 104_R | 2.202 | 0.99 |
| 281_D | 309_K | 2.149 | 0.99 |
| 379_R | 385_E | 2.071 | 0.98 |
| 87_I | 93_S | 2.024 | 0.98 |
| 45_I | 275_L | 1.959 | 0.97 |
| 195_V | 264_I | 1.957 | 0.97 |
| 218_R | 234_E | 1.879 | 0.97 |
| 79_W | 84_S | 1.861 | 0.96 |
| 116_Q | 250_M | 1.855 | 0.96 |
| 152_A | 268_F | 1.787 | 0.95 |
| 390_H | 405_G | 1.780 | 0.95 |
| 112_T | 151_E | 1.772 | 0.95 |
| 80_Q | 118_D | 1.767 | 0.95 |
| 195_V | 249_V | 1.752 | 0.94 |
| 341_V | 349_V | 1.752 | 0.94 |
| 341_V | 345_G | 1.738 | 0.94 |
| 155_L | 265_G | 1.716 | 0.93 |
| 43_W | 47_E | 1.676 | 0.92 |
| 52_H | 205_R | 1.642 | 0.91 |
| 235_I | 244_V | 1.603 | 0.90 |
| 323_I | 372_I | 1.581 | 0.89 |
| 313_L | 380_T | 1.550 | 0.88 |
| 396_A | 400_L | 1.527 | 0.87 |
| 369_C | 373_T | 1.498 | 0.85 |
| 220_V | 232_E | 1.497 | 0.85 |
| 310_F | 313_L | 1.479 | 0.84 |
| 355_I | 369_C | 1.467 | 0.84 |
| 142_Q | 242_L | 1.463 | 0.83 |
| 216_E | 236_N | 1.454 | 0.83 |
| 116_Q | 226_F | 1.446 | 0.82 |
| 374_Y | 390_H | 1.438 | 0.82 |
| 81_N | 85_L | 1.423 | 0.81 |
| 386_V | 390_H | 1.411 | 0.80 |
| 367_S | 371_R | 1.399 | 0.79 |
| 321_N | 383_Q | 1.398 | 0.79 |
| 367_S | 370_Y | 1.394 | 0.79 |
| 88_P | 223_Y | 1.389 | 0.79 |
| 356_D | 367_S | 1.388 | 0.79 |
| 120_L | 153_V | 1.361 | 0.77 |
| 116_Q | 129_V | 1.357 | 0.77 |
| 294_R | 315_K | 1.338 | 0.75 |
| 377_M | 380_T | 1.335 | 0.75 |
| 233_M | 244_V | 1.334 | 0.75 |
| 116_Q | 337_F | 1.324 | 0.74 |
| 46_K | 50_K | 1.323 | 0.74 |
| 403_V | 406_R | 1.320 | 0.74 |
| 341_V | 369_C | 1.315 | 0.73 |
| 169_E | 172_Q | 1.305 | 0.72 |
| 164_G | 167_D | 1.295 | 0.72 |
| 376_H | 383_Q | 1.289 | 0.71 |
| 345_G | 349_V | 1.284 | 0.71 |
| 177_S | 180_S | 1.271 | 0.70 |
| 323_I | 397_A | 1.266 | 0.69 |
| 139_I | 270_L | 1.265 | 0.69 |
| 29_R | 146_I | 1.255 | 0.68 |
| 365_K | 404_E | 1.255 | 0.68 |
| 373_T | 383_Q | 1.254 | 0.68 |
| 145_P | 299_F | 1.251 | 0.68 |
| 294_R | 310_F | 1.250 | 0.68 |
| 392_A | 395_E | 1.242 | 0.67 |
| 36_N | 46_K | 1.239 | 0.67 |
| 319_V | 383_Q | 1.230 | 0.66 |
| 193_K | 196_E | 1.228 | 0.66 |
| 377_M | 390_H | 1.227 | 0.66 |
| 103_N | 106_H | 1.227 | 0.66 |
| 179_R | 185_E | 1.219 | 0.65 |
| 294_R | 313_L | 1.215 | 0.65 |
| 176_Q | 180_S | 1.214 | 0.64 |
| 167_D | 175_E | 1.210 | 0.64 |
| 70_D | 130_V | 1.209 | 0.64 |
| 258_A | 312_P | 1.208 | 0.64 |
| 116_Q | 138_Q | 1.204 | 0.64 |
| 93_S | 110_A | 1.199 | 0.63 |
| 374_Y | 406_R | 1.198 | 0.63 |
| 8_E | 11_G | 1.194 | 0.63 |
| 290_C | 313_L | 1.193 | 0.62 |
| 179_R | 251_E | 1.191 | 0.62 |
| 300_C | 324_S | 1.190 | 0.62 |
| 321_N | 332_Y | 1.188 | 0.62 |
| 290_C | 296_L | 1.183 | 0.61 |
| 169_E | 186_T | 1.181 | 0.61 |
| 358_F | 367_S | 1.177 | 0.61 |
| 392_A | 396_A | 1.175 | 0.61 |
| 183_K | 188_T | 1.174 | 0.61 |
| 45_I | 377_M | 1.171 | 0.60 |
| 300_C | 306_Q | 1.159 | 0.59 |
| 395_E | 399_Q | 1.156 | 0.59 |
| 204_T | 217_I | 1.153 | 0.59 |
| 294_R | 318_A | 1.148 | 0.58 |
| 291_E | 327_L | 1.142 | 0.57 |
| 345_G | 386_V | 1.142 | 0.57 |
| 30_V | 33_N | 1.140 | 0.57 |
| 101_Y | 225_P | 1.137 | 0.57 |
| 39_H | 44_L | 1.128 | 0.56 |
| 171_L | 175_E | 1.128 | 0.56 |
| 297_K | 316_Y | 1.126 | 0.56 |
| 77_T | 106_H | 1.125 | 0.56 |
| 89_A | 206_L | 1.125 | 0.56 |
| 200_K | 279_L | 1.122 | 0.55 |
| 66_F | 168_G | 1.122 | 0.55 |
| 169_E | 213_D | 1.121 | 0.55 |
| 350_E | 375_R | 1.118 | 0.55 |
| 165_I | 169_E | 1.116 | 0.55 |
| 19_H | 106_H | 1.115 | 0.55 |
| 6_V | 185_E | 1.109 | 0.54 |
| 332_Y | 368_H | 1.108 | 0.54 |
| 332_Y | 337_F | 1.107 | 0.54 |
| 310_F | 315_K | 1.105 | 0.54 |
| 9_L | 102_L | 1.104 | 0.54 |
| 183_K | 189_M | 1.102 | 0.53 |
| 171_L | 174_F | 1.099 | 0.53 |
| 388_H | 392_A | 1.099 | 0.53 |
| 4_G | 8_E | 1.098 | 0.53 |
| 198_D | 339_D | 1.096 | 0.53 |
| 120_L | 131_G | 1.093 | 0.52 |
| 267_A | 274_R | 1.090 | 0.52 |
| 131_G | 153_V | 1.090 | 0.52 |
| 226_F | 375_R | 1.084 | 0.52 |
| 146_I | 354_L | 1.084 | 0.52 |
| 9_L | 27_L | 1.083 | 0.51 |
| 86_L | 251_E | 1.083 | 0.51 |
| 166_K | 169_E | 1.079 | 0.51 |
| 45_I | 378_E | 1.079 | 0.51 |
| 141_S | 240_E | 1.076 | 0.51 |
| 272_L | 366_T | 1.074 | 0.51 |
| 38_Q | 43_W | 1.072 | 0.50 |
| 94_R | 243_E | 1.070 | 0.50 |
| 207_M | 233_M | 1.069 | 0.50 |
| 367_S | 406_R | 1.068 | 0.50 |
| 358_F | 361_P | 1.066 | 0.50 |
| 217_I | 233_M | 1.064 | 0.50 |
| 381_L | 390_H | 1.060 | 0.49 |
| 188_T | 343_T | 1.059 | 0.49 |
| 252_Q | 256_N | 1.057 | 0.49 |
| 184_Q | 187_H | 1.056 | 0.49 |
| 42_L | 351_K | 1.056 | 0.49 |
| 310_F | 318_A | 1.056 | 0.49 |
| 318_A | 378_E | 1.056 | 0.49 |
| 349_V | 393_L | 1.053 | 0.48 |
| 72_L | 119_L | 1.052 | 0.48 |
| 196_E | 231_F | 1.051 | 0.48 |
| 391_Q | 405_G | 1.050 | 0.48 |
| 163_A | 167_D | 1.049 | 0.48 |
| 118_D | 122_A | 1.047 | 0.48 |
| 358_F | 371_R | 1.047 | 0.48 |
| 82_F | 91_H | 1.045 | 0.48 |
| 4_G | 9_L | 1.042 | 0.47 |
| 176_Q | 183_K | 1.041 | 0.47 |
| 112_T | 249_V | 1.041 | 0.47 |
| 94_R | 225_P | 1.040 | 0.47 |
| 114_A | 241_W | 1.034 | 0.46 |
| 19_H | 176_Q | 1.029 | 0.46 |
| 165_I | 171_L | 1.025 | 0.46 |
| 116_Q | 254_L | 1.024 | 0.45 |
| 73_S | 254_L | 1.024 | 0.45 |
| 164_G | 305_N | 1.023 | 0.45 |
| 183_K | 228_H | 1.023 | 0.45 |
| 206_L | 209_H | 1.020 | 0.45 |
| 130_V | 150_L | 1.019 | 0.45 |
| 170_S | 173_L | 1.019 | 0.45 |
| 186_T | 331_N | 1.017 | 0.45 |
| 132_D | 151_E | 1.014 | 0.44 |
| 155_L | 255_V | 1.013 | 0.44 |
| 240_E | 341_V | 1.013 | 0.44 |
| 180_S | 183_K | 1.012 | 0.44 |
| 38_Q | 352_V | 1.010 | 0.44 |
| 17_D | 104_R | 1.009 | 0.44 |
| 250_M | 265_G | 1.009 | 0.44 |
| 334_E | 368_H | 1.006 | 0.44 |
| 178_S | 183_K | 1.004 | 0.43 |
| 337_F | 340_L | 1.003 | 0.43 |
| 66_F | 257_S | 1.003 | 0.43 |
| 330_E | 344_I | 1.003 | 0.43 |
| 154_R | 235_I | 1.002 | 0.43 |
| 177_S | 183_K | 1.001 | 0.43 |
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 | |
| 3cmqA | 1 | 0.9951 | 100 | 0.417 | Contact Map |
| 1b7yA | 1 | 0.5749 | 100 | 0.702 | Contact Map |
| 4p72C | 2 | 0.5774 | 100 | 0.709 | Contact Map |
| 3pcoB | 2 | 0.8108 | 100 | 0.712 | Contact Map |
| 3pcoA | 2 | 0.6167 | 100 | 0.713 | Contact Map |
| 2rhqB | 1 | 0.7936 | 100 | 0.717 | Contact Map |
| 2du7A | 4 | 0.8084 | 100 | 0.722 | Contact Map |
| 4p72A | 2 | 0.7985 | 100 | 0.722 | Contact Map |
| 1b7yB | 1 | 0.7617 | 100 | 0.725 | Contact Map |
| 3l4gA | 8 | 0.6708 | 100 | 0.728 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)