| d4j07d_ |
| ID: | 1448379260 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (140) | ||
| Sequences: | 2570 (1356.5) | ||
| Seq/Len: | 18.357 | ||
| Nf(neff/√len): | 114.6 |
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: 18.357).
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 |
| 63_A | 134_A | 3.328 | 1.00 |
| 91_R | 95_D | 3.121 | 1.00 |
| 9_G | 57_L | 3.010 | 1.00 |
| 24_L | 41_V | 2.665 | 1.00 |
| 40_T | 61_H | 2.518 | 1.00 |
| 30_V | 128_A | 2.348 | 1.00 |
| 6_L | 138_A | 2.344 | 1.00 |
| 12_A | 24_L | 2.103 | 1.00 |
| 54_V | 66_A | 2.073 | 1.00 |
| 56_E | 145_R | 2.058 | 1.00 |
| 55_Q | 95_D | 2.016 | 1.00 |
| 18_R | 114_L | 2.012 | 1.00 |
| 66_A | 89_L | 1.926 | 1.00 |
| 42_V | 57_L | 1.907 | 1.00 |
| 50_I | 104_V | 1.835 | 1.00 |
| 28_R | 32_A | 1.831 | 1.00 |
| 84_S | 87_Q | 1.828 | 1.00 |
| 31_A | 36_I | 1.819 | 1.00 |
| 30_V | 132_A | 1.761 | 1.00 |
| 5_G | 38_G | 1.754 | 1.00 |
| 8_L | 138_A | 1.714 | 1.00 |
| 74_D | 115_D | 1.708 | 1.00 |
| 17_S | 21_D | 1.700 | 1.00 |
| 14_T | 136_T | 1.675 | 1.00 |
| 70_V | 81_V | 1.638 | 1.00 |
| 52_V | 141_L | 1.627 | 1.00 |
| 72_R | 108_N | 1.614 | 1.00 |
| 87_Q | 91_R | 1.603 | 1.00 |
| 126_K | 129_Q | 1.578 | 1.00 |
| 55_Q | 94_L | 1.521 | 1.00 |
| 6_L | 142_L | 1.490 | 1.00 |
| 76_P | 79_D | 1.488 | 1.00 |
| 12_A | 41_V | 1.481 | 1.00 |
| 56_E | 97_S | 1.481 | 1.00 |
| 101_G | 133_A | 1.479 | 1.00 |
| 44_V | 53_V | 1.466 | 1.00 |
| 85_V | 104_V | 1.449 | 1.00 |
| 52_V | 93_A | 1.437 | 1.00 |
| 22_A | 25_A | 1.422 | 1.00 |
| 19_I | 69_V | 1.408 | 1.00 |
| 31_A | 131_A | 1.392 | 0.99 |
| 18_R | 110_E | 1.384 | 0.99 |
| 11_V | 54_V | 1.359 | 0.99 |
| 48_I | 102_N | 1.356 | 0.99 |
| 21_D | 43_R | 1.351 | 0.99 |
| 111_K | 115_D | 1.279 | 0.99 |
| 17_S | 43_R | 1.244 | 0.98 |
| 101_G | 134_A | 1.236 | 0.98 |
| 108_N | 112_Q | 1.230 | 0.98 |
| 110_E | 119_L | 1.216 | 0.98 |
| 117_A | 125_D | 1.213 | 0.98 |
| 67_L | 103_G | 1.189 | 0.98 |
| 119_L | 123_A | 1.188 | 0.98 |
| 31_A | 65_V | 1.186 | 0.98 |
| 12_A | 20_C | 1.177 | 0.98 |
| 34_S | 135_L | 1.164 | 0.97 |
| 76_P | 80_Y | 1.153 | 0.97 |
| 29_K | 33_D | 1.148 | 0.97 |
| 25_A | 28_R | 1.148 | 0.97 |
| 78_F | 82_C | 1.139 | 0.97 |
| 9_G | 61_H | 1.108 | 0.96 |
| 51_P | 88_G | 1.103 | 0.96 |
| 54_V | 64_V | 1.102 | 0.96 |
| 56_E | 141_L | 1.099 | 0.96 |
| 58_A | 97_S | 1.082 | 0.96 |
| 53_V | 141_L | 1.069 | 0.95 |
| 79_D | 82_C | 1.066 | 0.95 |
| 70_V | 82_C | 1.066 | 0.95 |
| 25_A | 29_K | 1.065 | 0.95 |
| 101_G | 130_A | 1.053 | 0.95 |
| 19_I | 114_L | 1.040 | 0.94 |
| 72_R | 76_P | 1.039 | 0.94 |
| 55_Q | 97_S | 1.037 | 0.94 |
| 11_V | 50_I | 1.033 | 0.94 |
| 76_P | 108_N | 1.028 | 0.94 |
| 80_Y | 83_N | 1.017 | 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 | |
| 4j07A | 5 | 1 | 100 | 0.027 | Contact Map |
| 2c92A | 5 | 0.9932 | 100 | 0.03 | Contact Map |
| 1c41A | 10 | 1 | 100 | 0.038 | Contact Map |
| 3nq4A | 30 | 0.9726 | 100 | 0.041 | Contact Map |
| 1hqkA | 5 | 0.9795 | 100 | 0.042 | Contact Map |
| 1rvvA | 30 | 0.9795 | 100 | 0.045 | Contact Map |
| 2i0fA | 5 | 0.9589 | 100 | 0.049 | Contact Map |
| 1ejbA | 5 | 1 | 100 | 0.05 | Contact Map |
| 1c2yA | 20 | 0.9863 | 100 | 0.054 | Contact Map |
| 2obxA | 10 | 1 | 100 | 0.055 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)