| 1-350 |
| ID: | 1460555574 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 350 (164) | ||
| Sequences: | 9785 (5095.8) | ||
| Seq/Len: | 59.665 | ||
| Nf(neff/√len): | 397.9 |
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: 59.665).
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 |
| 239_H | 273_K | 4.730 | 1.00 |
| 38_F | 72_R | 2.873 | 1.00 |
| 41_G | 59_A | 2.729 | 1.00 |
| 226_R | 276_A | 2.701 | 1.00 |
| 26_D | 75_Q | 2.642 | 1.00 |
| 33_K | 37_G | 2.435 | 1.00 |
| 233_D | 238_G | 2.376 | 1.00 |
| 66_D | 71_G | 2.306 | 1.00 |
| 26_D | 30_H | 2.258 | 1.00 |
| 242_G | 260_A | 2.257 | 1.00 |
| 267_D | 272_G | 2.243 | 1.00 |
| 230_N | 236_M | 2.226 | 1.00 |
| 70_D | 77_E | 2.221 | 1.00 |
| 237_S | 244_Q | 2.164 | 1.00 |
| 267_D | 270_Q | 2.137 | 1.00 |
| 246_R | 256_Q | 2.060 | 1.00 |
| 276_A | 280_I | 1.947 | 1.00 |
| 18_T | 21_E | 1.897 | 1.00 |
| 271_D | 278_E | 1.851 | 1.00 |
| 35_I | 43_Q | 1.782 | 1.00 |
| 230_N | 276_A | 1.762 | 1.00 |
| 29_F | 33_K | 1.715 | 1.00 |
| 22_R | 79_S | 1.689 | 1.00 |
| 242_G | 263_W | 1.657 | 1.00 |
| 235_T | 244_Q | 1.640 | 1.00 |
| 66_D | 70_D | 1.621 | 1.00 |
| 75_Q | 79_S | 1.616 | 1.00 |
| 267_D | 271_D | 1.535 | 1.00 |
| 267_D | 278_E | 1.522 | 1.00 |
| 279_F | 283_M | 1.499 | 1.00 |
| 233_D | 236_M | 1.493 | 1.00 |
| 255_P | 258_Q | 1.484 | 1.00 |
| 17_I | 21_E | 1.452 | 1.00 |
| 45_R | 49_F | 1.444 | 1.00 |
| 240_L | 245_A | 1.434 | 1.00 |
| 66_D | 69_N | 1.424 | 1.00 |
| 40_T | 43_Q | 1.396 | 0.99 |
| 246_R | 250_M | 1.369 | 0.99 |
| 233_D | 244_Q | 1.356 | 0.99 |
| 275_T | 278_E | 1.353 | 0.99 |
| 68_N | 77_E | 1.347 | 0.99 |
| 74_D | 77_E | 1.319 | 0.99 |
| 45_R | 58_L | 1.302 | 0.99 |
| 234_K | 247_T | 1.284 | 0.99 |
| 32_L | 47_F | 1.277 | 0.99 |
| 226_R | 230_N | 1.240 | 0.98 |
| 41_G | 62_W | 1.240 | 0.98 |
| 239_H | 275_T | 1.231 | 0.98 |
| 246_R | 260_A | 1.226 | 0.98 |
| 271_D | 275_T | 1.201 | 0.98 |
| 242_G | 246_R | 1.191 | 0.98 |
| 266_S | 274_L | 1.185 | 0.98 |
| 241_T | 273_K | 1.184 | 0.98 |
| 22_R | 26_D | 1.181 | 0.98 |
| 29_F | 78_F | 1.173 | 0.98 |
| 269_D | 275_T | 1.173 | 0.98 |
| 17_I | 22_R | 1.166 | 0.97 |
| 66_D | 77_E | 1.150 | 0.97 |
| 233_D | 237_S | 1.149 | 0.97 |
| 222_R | 226_R | 1.136 | 0.97 |
| 279_F | 282_A | 1.135 | 0.97 |
| 45_R | 55_Q | 1.134 | 0.97 |
| 226_R | 280_I | 1.131 | 0.97 |
| 241_T | 244_Q | 1.130 | 0.97 |
| 239_H | 271_D | 1.120 | 0.96 |
| 232_H | 248_I | 1.119 | 0.96 |
| 44_A | 62_W | 1.109 | 0.96 |
| 19_V | 22_R | 1.100 | 0.96 |
| 60_Q | 63_A | 1.094 | 0.96 |
| 268_I | 281_L | 1.093 | 0.96 |
| 237_S | 241_T | 1.093 | 0.96 |
| 30_H | 75_Q | 1.090 | 0.96 |
| 33_K | 39_I | 1.088 | 0.96 |
| 33_K | 43_Q | 1.085 | 0.96 |
| 19_V | 23_A | 1.075 | 0.95 |
| 25_H | 82_M | 1.059 | 0.95 |
| 263_W | 267_D | 1.051 | 0.94 |
| 95_P | 99_P | 1.026 | 0.94 |
| 34_P | 43_Q | 1.016 | 0.93 |
| 65_A | 73_M | 1.015 | 0.93 |
| 229_F | 233_D | 1.006 | 0.93 |
| 39_I | 44_A | 1.005 | 0.93 |
| 231_S | 248_I | 1.004 | 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 | |
| 4cidA | 1 | 0.2886 | 99.9 | 0.676 | Contact Map |
| 2jq6A | 1 | 0.3943 | 99.9 | 0.708 | Contact Map |
| 3q5iA | 1 | 0.4457 | 99.8 | 0.717 | Contact Map |
| 4qoxA | 1 | 0.4514 | 99.8 | 0.72 | Contact Map |
| 3lijA | 1 | 0.4514 | 99.8 | 0.723 | Contact Map |
| 3u0kA | 1 | 0.4229 | 99.8 | 0.724 | Contact Map |
| 3nyvA | 1 | 0.44 | 99.8 | 0.727 | Contact Map |
| 3mwuA | 1 | 0.3971 | 99.8 | 0.729 | Contact Map |
| 4i2yA | 2 | 0.4371 | 99.8 | 0.73 | Contact Map |
| 4mvfA | 1 | 0.4429 | 99.8 | 0.731 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)