| t_coffee_200 |
| ID: | 1446004713 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 398 (300) | ||
| Sequences: | 38292 (22657.4) | ||
| Seq/Len: | 127.640 | ||
| Nf(neff/√len): | 1308.1 |
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: 127.640).
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 | 4.741 | 1.00 |
| 187_I | 210_A | 4.420 | 1.00 |
| 150_P | 172_V | 4.347 | 1.00 |
| 127_I | 385_K | 3.493 | 1.00 |
| 346_P | 370_A | 3.315 | 1.00 |
| 380_R | 383_E | 3.231 | 1.00 |
| 341_G | 391_F | 3.214 | 1.00 |
| 174_D | 201_L | 3.160 | 1.00 |
| 367_R | 387_D | 3.125 | 1.00 |
| 187_I | 209_K | 2.723 | 1.00 |
| 214_N | 384_L | 2.717 | 1.00 |
| 174_D | 205_F | 2.509 | 1.00 |
| 141_P | 389_T | 2.439 | 1.00 |
| 95_T | 156_S | 2.371 | 1.00 |
| 184_S | 209_K | 2.363 | 1.00 |
| 188_I | 198_G | 2.363 | 1.00 |
| 177_M | 186_Y | 2.352 | 1.00 |
| 372_G | 380_R | 2.303 | 1.00 |
| 369_H | 387_D | 2.295 | 1.00 |
| 346_P | 368_D | 2.230 | 1.00 |
| 201_L | 205_F | 2.215 | 1.00 |
| 174_D | 178_K | 2.197 | 1.00 |
| 195_S | 216_C | 2.193 | 1.00 |
| 147_P | 173_V | 2.127 | 1.00 |
| 187_I | 392_V | 2.122 | 1.00 |
| 171_R | 204_G | 2.046 | 1.00 |
| 365_F | 394_Q | 2.011 | 1.00 |
| 97_H | 154_F | 2.003 | 1.00 |
| 130_L | 385_K | 1.994 | 1.00 |
| 98_F | 176_L | 1.965 | 1.00 |
| 200_L | 204_G | 1.944 | 1.00 |
| 215_L | 348_D | 1.925 | 1.00 |
| 110_P | 145_V | 1.918 | 1.00 |
| 187_I | 212_H | 1.913 | 1.00 |
| 128_L | 146_V | 1.885 | 1.00 |
| 99_A | 121_F | 1.884 | 1.00 |
| 212_H | 388_L | 1.870 | 1.00 |
| 113_L | 189_Q | 1.870 | 1.00 |
| 198_G | 211_V | 1.846 | 1.00 |
| 109_V | 187_I | 1.819 | 1.00 |
| 149_L | 197_V | 1.817 | 1.00 |
| 210_A | 395_V | 1.816 | 1.00 |
| 386_T | 390_A | 1.797 | 1.00 |
| 114_L | 198_G | 1.795 | 1.00 |
| 202_G | 211_V | 1.786 | 1.00 |
| 170_A | 200_L | 1.766 | 1.00 |
| 387_D | 390_A | 1.737 | 1.00 |
| 383_E | 387_D | 1.722 | 1.00 |
| 167_M | 204_G | 1.692 | 1.00 |
| 112_A | 177_M | 1.687 | 1.00 |
| 173_V | 201_L | 1.677 | 1.00 |
| 110_P | 143_H | 1.671 | 1.00 |
| 100_A | 145_V | 1.654 | 1.00 |
| 142_F | 187_I | 1.632 | 1.00 |
| 119_G | 123_E | 1.630 | 1.00 |
| 114_L | 149_L | 1.624 | 1.00 |
| 145_V | 176_L | 1.620 | 1.00 |
| 178_K | 207_A | 1.617 | 1.00 |
| 332_K | 335_Y | 1.604 | 1.00 |
| 341_G | 367_R | 1.596 | 1.00 |
| 113_L | 144_L | 1.587 | 1.00 |
| 90_E | 95_T | 1.559 | 1.00 |
| 115_H | 152_Y | 1.554 | 1.00 |
| 97_H | 121_F | 1.544 | 1.00 |
| 114_L | 173_V | 1.539 | 1.00 |
| 121_F | 154_F | 1.527 | 1.00 |
| 353_P | 368_D | 1.521 | 1.00 |
| 369_H | 372_G | 1.520 | 1.00 |
| 147_P | 176_L | 1.517 | 1.00 |
| 115_H | 149_L | 1.507 | 1.00 |
| 201_L | 208_C | 1.490 | 1.00 |
| 177_M | 182_F | 1.464 | 1.00 |
| 110_P | 182_F | 1.441 | 1.00 |
| 148_S | 153_T | 1.439 | 1.00 |
| 212_H | 341_G | 1.431 | 1.00 |
| 140_L | 389_T | 1.425 | 1.00 |
| 343_S | 369_H | 1.414 | 1.00 |
| 165_G | 168_D | 1.411 | 1.00 |
| 384_L | 388_L | 1.409 | 1.00 |
| 200_L | 203_V | 1.398 | 0.99 |
| 189_Q | 214_N | 1.396 | 0.99 |
| 189_Q | 388_L | 1.393 | 0.99 |
| 130_L | 389_T | 1.388 | 0.99 |
| 191_G | 377_A | 1.387 | 0.99 |
| 96_I | 172_V | 1.363 | 0.99 |
| 121_F | 148_S | 1.351 | 0.99 |
| 177_M | 201_L | 1.349 | 0.99 |
| 346_P | 371_E | 1.348 | 0.99 |
| 213_L | 216_C | 1.328 | 0.99 |
| 130_L | 382_R | 1.320 | 0.99 |
| 142_F | 393_E | 1.309 | 0.99 |
| 182_F | 186_Y | 1.309 | 0.99 |
| 211_V | 340_F | 1.308 | 0.99 |
| 101_L | 146_V | 1.304 | 0.99 |
| 109_V | 209_K | 1.301 | 0.99 |
| 96_I | 155_S | 1.297 | 0.99 |
| 92_E | 175_Q | 1.296 | 0.99 |
| 343_S | 387_D | 1.287 | 0.99 |
| 383_E | 386_T | 1.278 | 0.99 |
| 188_I | 201_L | 1.276 | 0.99 |
| 344_F | 368_D | 1.263 | 0.99 |
| 112_A | 173_V | 1.260 | 0.99 |
| 382_R | 386_T | 1.237 | 0.98 |
| 111_I | 142_F | 1.229 | 0.98 |
| 125_Y | 146_V | 1.224 | 0.98 |
| 112_A | 186_Y | 1.222 | 0.98 |
| 132_R | 144_L | 1.221 | 0.98 |
| 118_P | 152_Y | 1.215 | 0.98 |
| 343_S | 384_L | 1.212 | 0.98 |
| 116_G | 192_D | 1.208 | 0.98 |
| 176_L | 180_L | 1.208 | 0.98 |
| 367_R | 390_A | 1.201 | 0.98 |
| 191_G | 375_F | 1.200 | 0.98 |
| 142_F | 392_V | 1.188 | 0.98 |
| 190_G | 198_G | 1.174 | 0.98 |
| 97_H | 148_S | 1.170 | 0.97 |
| 170_A | 197_V | 1.168 | 0.97 |
| 118_P | 192_D | 1.164 | 0.97 |
| 141_P | 393_E | 1.164 | 0.97 |
| 203_V | 332_K | 1.163 | 0.97 |
| 340_F | 360_T | 1.153 | 0.97 |
| 94_L | 150_P | 1.137 | 0.97 |
| 111_I | 189_Q | 1.136 | 0.97 |
| 372_G | 379_E | 1.134 | 0.97 |
| 126_P | 129_Q | 1.131 | 0.97 |
| 199_R | 213_L | 1.130 | 0.97 |
| 174_D | 204_G | 1.124 | 0.97 |
| 108_A | 143_H | 1.121 | 0.97 |
| 167_M | 200_L | 1.120 | 0.96 |
| 369_H | 383_E | 1.117 | 0.96 |
| 192_D | 374_H | 1.117 | 0.96 |
| 88_T | 95_T | 1.115 | 0.96 |
| 114_L | 147_P | 1.114 | 0.96 |
| 372_G | 376_A | 1.114 | 0.96 |
| 360_T | 364_V | 1.110 | 0.96 |
| 189_Q | 212_H | 1.108 | 0.96 |
| 114_L | 188_I | 1.089 | 0.96 |
| 121_F | 146_V | 1.078 | 0.95 |
| 347_K | 371_E | 1.078 | 0.95 |
| 111_I | 131_F | 1.073 | 0.95 |
| 150_P | 169_N | 1.069 | 0.95 |
| 123_E | 377_A | 1.068 | 0.95 |
| 145_V | 180_L | 1.059 | 0.95 |
| 373_G | 379_E | 1.055 | 0.95 |
| 149_L | 193_I | 1.052 | 0.95 |
| 357_I | 364_V | 1.051 | 0.94 |
| 365_F | 390_A | 1.048 | 0.94 |
| 389_T | 393_E | 1.043 | 0.94 |
| 365_F | 387_D | 1.042 | 0.94 |
| 128_L | 144_L | 1.031 | 0.94 |
| 377_A | 384_L | 1.018 | 0.93 |
| 344_F | 353_P | 1.018 | 0.93 |
| 369_H | 380_R | 1.017 | 0.93 |
| 168_D | 171_R | 1.007 | 0.93 |
| 385_K | 389_T | 1.001 | 0.92 |
| 113_L | 131_F | 1.000 | 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 | |
| 3g02A | 2 | 0.9648 | 100 | 0.118 | Contact Map |
| 4qa9A | 1 | 0.9447 | 100 | 0.173 | Contact Map |
| 4qlaA | 2 | 0.9749 | 100 | 0.181 | Contact Map |
| 1ehyA | 4 | 0.6809 | 100 | 0.497 | Contact Map |
| 4inzA | 2 | 0.701 | 100 | 0.53 | Contact Map |
| 3r40A | 2 | 0.706 | 100 | 0.536 | Contact Map |
| 5bovA | 4 | 0 | 100 | 0.542 | Contact Map |
| 4psuA | 1 | 0.7085 | 100 | 0.548 | Contact Map |
| 3oosA | 1 | 0.6683 | 100 | 0.552 | Contact Map |
| 2pujA | 1 | 0.6709 | 100 | 0.554 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)