| muscle_400_epoxide |
| ID: | 1445524143 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 398 (306) | ||
| Sequences: | 43996 (28064.1) | ||
| Seq/Len: | 143.778 | ||
| Nf(neff/√len): | 1604.3 |
HHblits Results: (2015_06)
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: 143.778).
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 |
| 100_A | 143_H | 4.891 | 1.00 |
| 150_P | 172_V | 4.277 | 1.00 |
| 346_P | 370_A | 3.621 | 1.00 |
| 341_G | 391_F | 3.516 | 1.00 |
| 174_D | 201_L | 3.476 | 1.00 |
| 127_I | 385_K | 3.444 | 1.00 |
| 380_R | 383_E | 3.416 | 1.00 |
| 187_I | 210_A | 3.392 | 1.00 |
| 367_R | 387_D | 3.235 | 1.00 |
| 369_H | 387_D | 2.757 | 1.00 |
| 188_I | 198_G | 2.749 | 1.00 |
| 174_D | 205_F | 2.595 | 1.00 |
| 174_D | 178_K | 2.479 | 1.00 |
| 346_P | 368_D | 2.455 | 1.00 |
| 95_T | 156_S | 2.419 | 1.00 |
| 187_I | 392_V | 2.338 | 1.00 |
| 177_M | 186_Y | 2.333 | 1.00 |
| 141_P | 389_T | 2.294 | 1.00 |
| 372_G | 380_R | 2.251 | 1.00 |
| 99_A | 121_F | 2.227 | 1.00 |
| 97_H | 154_F | 2.227 | 1.00 |
| 185_G | 209_K | 2.155 | 1.00 |
| 200_L | 204_G | 2.133 | 1.00 |
| 130_L | 385_K | 2.121 | 1.00 |
| 98_F | 176_L | 2.107 | 1.00 |
| 201_L | 205_F | 2.080 | 1.00 |
| 110_P | 145_V | 2.062 | 1.00 |
| 140_L | 389_T | 2.040 | 1.00 |
| 365_F | 394_Q | 2.018 | 1.00 |
| 171_R | 204_G | 1.978 | 1.00 |
| 170_A | 200_L | 1.960 | 1.00 |
| 110_P | 143_H | 1.950 | 1.00 |
| 147_P | 173_V | 1.938 | 1.00 |
| 187_I | 209_K | 1.898 | 1.00 |
| 387_D | 390_A | 1.877 | 1.00 |
| 383_E | 387_D | 1.871 | 1.00 |
| 386_T | 390_A | 1.868 | 1.00 |
| 109_V | 187_I | 1.850 | 1.00 |
| 114_L | 149_L | 1.839 | 1.00 |
| 114_L | 173_V | 1.818 | 1.00 |
| 113_L | 189_Q | 1.803 | 1.00 |
| 187_I | 211_V | 1.784 | 1.00 |
| 100_A | 145_V | 1.773 | 1.00 |
| 101_L | 146_V | 1.763 | 1.00 |
| 149_L | 197_V | 1.756 | 1.00 |
| 128_L | 146_V | 1.729 | 1.00 |
| 341_G | 367_R | 1.720 | 1.00 |
| 178_K | 208_C | 1.717 | 1.00 |
| 97_H | 121_F | 1.715 | 1.00 |
| 167_M | 204_G | 1.711 | 1.00 |
| 114_L | 198_G | 1.686 | 1.00 |
| 112_A | 177_M | 1.666 | 1.00 |
| 216_C | 348_D | 1.660 | 1.00 |
| 202_G | 211_V | 1.650 | 1.00 |
| 121_F | 154_F | 1.649 | 1.00 |
| 173_V | 201_L | 1.646 | 1.00 |
| 369_H | 372_G | 1.635 | 1.00 |
| 142_F | 187_I | 1.632 | 1.00 |
| 187_I | 212_H | 1.627 | 1.00 |
| 119_G | 123_E | 1.609 | 1.00 |
| 353_P | 368_D | 1.564 | 1.00 |
| 332_K | 335_Y | 1.554 | 1.00 |
| 96_I | 172_V | 1.550 | 1.00 |
| 115_H | 152_Y | 1.548 | 1.00 |
| 130_L | 389_T | 1.518 | 1.00 |
| 383_E | 386_T | 1.510 | 1.00 |
| 110_P | 182_F | 1.498 | 1.00 |
| 115_H | 149_L | 1.493 | 1.00 |
| 214_N | 384_L | 1.489 | 1.00 |
| 90_E | 95_T | 1.487 | 1.00 |
| 200_L | 203_V | 1.486 | 1.00 |
| 121_F | 148_S | 1.472 | 1.00 |
| 116_G | 192_D | 1.471 | 1.00 |
| 145_V | 176_L | 1.471 | 1.00 |
| 147_P | 176_L | 1.469 | 1.00 |
| 113_L | 144_L | 1.452 | 1.00 |
| 130_L | 382_R | 1.444 | 1.00 |
| 343_S | 369_H | 1.424 | 1.00 |
| 111_I | 142_F | 1.422 | 1.00 |
| 165_G | 168_D | 1.421 | 1.00 |
| 343_S | 387_D | 1.414 | 1.00 |
| 148_S | 153_T | 1.406 | 0.99 |
| 198_G | 211_V | 1.398 | 0.99 |
| 346_P | 371_E | 1.395 | 0.99 |
| 142_F | 393_E | 1.391 | 0.99 |
| 192_D | 374_H | 1.385 | 0.99 |
| 191_G | 377_A | 1.371 | 0.99 |
| 211_V | 215_L | 1.364 | 0.99 |
| 384_L | 388_L | 1.343 | 0.99 |
| 364_V | 394_Q | 1.338 | 0.99 |
| 92_E | 175_Q | 1.336 | 0.99 |
| 195_S | 217_A | 1.329 | 0.99 |
| 190_G | 198_G | 1.325 | 0.99 |
| 382_R | 386_T | 1.320 | 0.99 |
| 191_G | 375_F | 1.311 | 0.99 |
| 389_T | 393_E | 1.286 | 0.99 |
| 210_A | 395_V | 1.279 | 0.99 |
| 182_F | 185_G | 1.278 | 0.99 |
| 189_Q | 388_L | 1.270 | 0.99 |
| 182_F | 186_Y | 1.264 | 0.99 |
| 372_G | 376_A | 1.260 | 0.99 |
| 142_F | 392_V | 1.259 | 0.99 |
| 344_F | 368_D | 1.256 | 0.99 |
| 360_T | 363_L | 1.254 | 0.99 |
| 203_V | 332_K | 1.253 | 0.99 |
| 114_L | 147_P | 1.253 | 0.99 |
| 97_H | 148_S | 1.248 | 0.99 |
| 121_F | 146_V | 1.238 | 0.98 |
| 357_I | 363_L | 1.237 | 0.98 |
| 177_M | 201_L | 1.235 | 0.98 |
| 189_Q | 214_N | 1.222 | 0.98 |
| 367_R | 390_A | 1.217 | 0.98 |
| 347_K | 371_E | 1.213 | 0.98 |
| 340_F | 360_T | 1.209 | 0.98 |
| 188_I | 201_L | 1.209 | 0.98 |
| 167_M | 200_L | 1.206 | 0.98 |
| 141_P | 393_E | 1.192 | 0.98 |
| 170_A | 197_V | 1.177 | 0.98 |
| 123_E | 377_A | 1.177 | 0.98 |
| 103_S | 143_H | 1.171 | 0.98 |
| 102_F | 143_H | 1.170 | 0.97 |
| 176_L | 180_L | 1.168 | 0.97 |
| 177_M | 182_F | 1.159 | 0.97 |
| 372_G | 379_E | 1.150 | 0.97 |
| 94_L | 150_P | 1.135 | 0.97 |
| 343_S | 384_L | 1.131 | 0.97 |
| 367_R | 383_E | 1.128 | 0.97 |
| 185_G | 210_A | 1.127 | 0.97 |
| 96_I | 155_S | 1.125 | 0.97 |
| 212_H | 388_L | 1.125 | 0.97 |
| 190_G | 195_S | 1.124 | 0.97 |
| 365_F | 387_D | 1.118 | 0.96 |
| 168_D | 171_R | 1.104 | 0.96 |
| 205_F | 208_C | 1.103 | 0.96 |
| 125_Y | 146_V | 1.101 | 0.96 |
| 174_D | 204_G | 1.094 | 0.96 |
| 174_D | 208_C | 1.092 | 0.96 |
| 118_P | 152_Y | 1.092 | 0.96 |
| 114_L | 188_I | 1.091 | 0.96 |
| 130_L | 140_L | 1.090 | 0.96 |
| 112_A | 186_Y | 1.089 | 0.96 |
| 385_K | 389_T | 1.087 | 0.96 |
| 369_H | 383_E | 1.077 | 0.95 |
| 126_P | 129_Q | 1.074 | 0.95 |
| 181_G | 184_S | 1.071 | 0.95 |
| 201_L | 208_C | 1.069 | 0.95 |
| 94_L | 156_S | 1.065 | 0.95 |
| 178_K | 205_F | 1.062 | 0.95 |
| 112_A | 173_V | 1.046 | 0.94 |
| 344_F | 353_P | 1.046 | 0.94 |
| 199_R | 213_L | 1.045 | 0.94 |
| 175_Q | 178_K | 1.045 | 0.94 |
| 373_G | 379_E | 1.037 | 0.94 |
| 109_V | 185_G | 1.035 | 0.94 |
| 111_I | 392_V | 1.034 | 0.94 |
| 111_I | 144_L | 1.032 | 0.94 |
| 170_A | 201_L | 1.032 | 0.94 |
| 200_L | 332_K | 1.032 | 0.94 |
| 345_F | 376_A | 1.030 | 0.94 |
| 118_P | 192_D | 1.023 | 0.93 |
| 142_F | 389_T | 1.022 | 0.93 |
| 175_Q | 179_D | 1.014 | 0.93 |
| 171_R | 174_D | 1.011 | 0.93 |
| 149_L | 193_I | 1.005 | 0.93 |
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 | |
| 3g02A | 2 | 0.9698 | 100 | 0.065 | Contact Map |
| 4qa9A | 1 | 0.9447 | 100 | 0.137 | Contact Map |
| 4qlaA | 2 | 0.9673 | 100 | 0.147 | Contact Map |
| 1ehyA | 4 | 0.6834 | 100 | 0.476 | Contact Map |
| 4inzA | 2 | 0.7035 | 100 | 0.503 | Contact Map |
| 3r40A | 2 | 0.7111 | 100 | 0.51 | Contact Map |
| 5bovA | 4 | 0 | 100 | 0.517 | Contact Map |
| 4psuA | 1 | 0.7111 | 100 | 0.523 | Contact Map |
| 3qyjA | 2 | 0.706 | 100 | 0.528 | Contact Map |
| 3oosA | 1 | 0.6859 | 100 | 0.528 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)