| 2yjm |
| ID: | 1492603639 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 176 (151) | ||
| Sequences: | 791 (503.4) | ||
| Seq/Len: | 5.238 | ||
| Nf(neff/√len): | 41.0 |
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: 5.238).
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 |
| 78_Y | 99_F | 3.479 | 1.00 |
| 83_F | 102_K | 2.662 | 1.00 |
| 75_K | 90_A | 2.456 | 1.00 |
| 93_I | 138_V | 2.419 | 1.00 |
| 11_Y | 15_S | 2.114 | 1.00 |
| 16_K | 105_E | 2.045 | 1.00 |
| 65_S | 89_H | 2.028 | 1.00 |
| 93_I | 141_L | 2.020 | 1.00 |
| 28_P | 33_E | 1.928 | 1.00 |
| 22_F | 93_I | 1.839 | 1.00 |
| 15_S | 153_F | 1.626 | 0.99 |
| 142_P | 150_V | 1.597 | 0.99 |
| 16_K | 101_S | 1.559 | 0.99 |
| 151_R | 155_R | 1.557 | 0.99 |
| 101_S | 105_E | 1.553 | 0.99 |
| 73_V | 134_L | 1.518 | 0.99 |
| 65_S | 68_E | 1.492 | 0.99 |
| 22_F | 147_L | 1.450 | 0.98 |
| 22_F | 150_V | 1.438 | 0.98 |
| 145_P | 149_F | 1.431 | 0.98 |
| 26_A | 47_S | 1.426 | 0.98 |
| 11_Y | 126_Q | 1.420 | 0.98 |
| 70_Y | 144_A | 1.391 | 0.97 |
| 138_V | 154_V | 1.369 | 0.97 |
| 20_H | 159_K | 1.362 | 0.97 |
| 67_A | 133_H | 1.342 | 0.97 |
| 63_P | 70_Y | 1.336 | 0.97 |
| 15_S | 126_Q | 1.328 | 0.96 |
| 15_S | 157_D | 1.325 | 0.96 |
| 17_I | 34_I | 1.297 | 0.96 |
| 155_R | 163_S | 1.279 | 0.95 |
| 11_Y | 157_D | 1.279 | 0.95 |
| 104_V | 126_Q | 1.274 | 0.95 |
| 68_E | 89_H | 1.270 | 0.95 |
| 129_F | 136_P | 1.265 | 0.95 |
| 16_K | 98_A | 1.262 | 0.95 |
| 20_H | 27_I | 1.240 | 0.94 |
| 20_H | 24_D | 1.227 | 0.94 |
| 67_A | 71_E | 1.210 | 0.93 |
| 100_M | 153_F | 1.207 | 0.93 |
| 11_Y | 100_M | 1.206 | 0.93 |
| 100_M | 126_Q | 1.196 | 0.93 |
| 56_S | 59_I | 1.178 | 0.92 |
| 29_K | 33_E | 1.154 | 0.91 |
| 110_L | 124_A | 1.145 | 0.90 |
| 67_A | 96_E | 1.141 | 0.90 |
| 23_Y | 95_V | 1.141 | 0.90 |
| 18_F | 141_L | 1.131 | 0.90 |
| 74_M | 96_E | 1.119 | 0.89 |
| 7_R | 160_Y | 1.090 | 0.87 |
| 22_F | 146_L | 1.087 | 0.87 |
| 19_Y | 56_S | 1.084 | 0.87 |
| 48_V | 51_R | 1.075 | 0.86 |
| 66_L | 89_H | 1.063 | 0.85 |
| 92_H | 141_L | 1.060 | 0.85 |
| 80_R | 148_N | 1.045 | 0.84 |
| 14_L | 38_F | 1.044 | 0.84 |
| 58_L | 94_A | 1.022 | 0.82 |
| 53_L | 58_L | 1.021 | 0.82 |
| 71_E | 90_A | 1.011 | 0.81 |
| 79_E | 138_V | 1.001 | 0.80 |
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 | |
| 2xolA | 2 | 0.9489 | 100 | 0.295 | Contact Map |
| 1s9uA | 1 | 0.8693 | 99.9 | 0.478 | Contact Map |
| 1n1cA | 2 | 0.8523 | 99.8 | 0.503 | Contact Map |
| 2o9xA | 1 | 0.7273 | 99.7 | 0.571 | Contact Map |
| 3lxuX | 1 | 0.3693 | 4 | 0.949 | Contact Map |
| 2hh6A | 1 | 0.625 | 2.8 | 0.953 | Contact Map |
| 4k5aA | 1 | 0.8352 | 2.5 | 0.954 | Contact Map |
| 1otkA | 2 | 0.4773 | 2.5 | 0.954 | Contact Map |
| 3nkeA | 3 | 0.4261 | 2.4 | 0.954 | Contact Map |
| 1mtyB | 2 | 0.5455 | 2.4 | 0.955 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)