| 4e9e |
| ID: | 1492603749 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 152 (131) | ||
| Sequences: | 2429 (1577.6) | ||
| Seq/Len: | 18.542 | ||
| Nf(neff/√len): | 137.8 |
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: 18.542).
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 |
| 36_I | 91_I | 2.489 | 1.00 |
| 32_W | 63_A | 2.319 | 1.00 |
| 70_D | 73_D | 2.237 | 1.00 |
| 86_L | 90_T | 2.193 | 1.00 |
| 75_S | 85_D | 2.167 | 1.00 |
| 96_D | 100_T | 2.131 | 1.00 |
| 71_W | 88_A | 2.032 | 1.00 |
| 86_L | 89_K | 1.985 | 1.00 |
| 35_L | 120_Y | 1.943 | 1.00 |
| 62_S | 65_V | 1.854 | 1.00 |
| 112_I | 116_G | 1.849 | 1.00 |
| 59_K | 73_D | 1.844 | 1.00 |
| 32_W | 95_S | 1.821 | 1.00 |
| 39_I | 94_F | 1.818 | 1.00 |
| 64_E | 99_L | 1.775 | 1.00 |
| 112_I | 117_N | 1.722 | 1.00 |
| 48_M | 51_P | 1.625 | 1.00 |
| 56_F | 66_A | 1.615 | 1.00 |
| 35_L | 94_F | 1.561 | 1.00 |
| 54_W | 58_E | 1.548 | 1.00 |
| 51_P | 55_K | 1.536 | 1.00 |
| 71_W | 92_V | 1.521 | 1.00 |
| 42_N | 116_G | 1.507 | 1.00 |
| 92_V | 96_D | 1.497 | 1.00 |
| 67_R | 96_D | 1.478 | 1.00 |
| 114_K | 118_D | 1.478 | 1.00 |
| 89_K | 110_H | 1.452 | 1.00 |
| 93_K | 97_E | 1.428 | 1.00 |
| 97_E | 101_K | 1.415 | 1.00 |
| 63_A | 99_L | 1.407 | 0.99 |
| 96_D | 99_L | 1.403 | 0.99 |
| 118_D | 133_P | 1.402 | 0.99 |
| 69_A | 74_V | 1.402 | 0.99 |
| 115_Y | 137_K | 1.374 | 0.99 |
| 71_W | 89_K | 1.353 | 0.99 |
| 40_F | 56_F | 1.321 | 0.99 |
| 60_Y | 69_A | 1.315 | 0.99 |
| 97_E | 110_H | 1.294 | 0.99 |
| 53_L | 57_L | 1.287 | 0.99 |
| 55_K | 58_E | 1.283 | 0.99 |
| 45_S | 48_M | 1.270 | 0.99 |
| 40_F | 53_L | 1.262 | 0.99 |
| 84_Y | 87_R | 1.253 | 0.99 |
| 71_W | 75_S | 1.234 | 0.98 |
| 67_R | 99_L | 1.230 | 0.98 |
| 93_K | 110_H | 1.218 | 0.98 |
| 41_L | 46_G | 1.205 | 0.98 |
| 39_I | 90_T | 1.203 | 0.98 |
| 67_R | 92_V | 1.197 | 0.98 |
| 94_F | 109_L | 1.195 | 0.98 |
| 63_A | 95_S | 1.184 | 0.98 |
| 126_N | 129_K | 1.173 | 0.98 |
| 127_E | 130_Q | 1.168 | 0.97 |
| 89_K | 93_K | 1.156 | 0.97 |
| 44_T | 82_G | 1.153 | 0.97 |
| 31_P | 120_Y | 1.122 | 0.97 |
| 78_L | 91_I | 1.093 | 0.96 |
| 90_T | 110_H | 1.091 | 0.96 |
| 97_E | 102_Q | 1.083 | 0.96 |
| 76_E | 79_K | 1.082 | 0.96 |
| 41_L | 115_Y | 1.075 | 0.95 |
| 97_E | 109_L | 1.058 | 0.95 |
| 121_R | 127_E | 1.053 | 0.95 |
| 28_F | 34_L | 1.048 | 0.94 |
| 122_I | 131_V | 1.041 | 0.94 |
| 107_I | 117_N | 1.035 | 0.94 |
| 93_K | 96_D | 1.033 | 0.94 |
| 34_L | 124_C | 1.023 | 0.93 |
| 50_I | 54_W | 1.019 | 0.93 |
| 41_L | 81_L | 1.015 | 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 | |
| 4ofaA | 1 | 0 | 100 | 0.207 | Contact Map |
| 2yg9A | 2 | 0.9605 | 100 | 0.316 | Contact Map |
| 2h56A | 3 | 0.9671 | 100 | 0.321 | Contact Map |
| 4b21A | 1 | 0.9671 | 100 | 0.324 | Contact Map |
| 4unfA | 1 | 0 | 100 | 0.337 | Contact Map |
| 3i0wA | 1 | 0.9539 | 99.9 | 0.354 | Contact Map |
| 1ornA | 1 | 0.9737 | 99.9 | 0.356 | Contact Map |
| 4ejyA | 2 | 0.9474 | 99.9 | 0.356 | Contact Map |
| 4uobA | 1 | 0 | 99.9 | 0.356 | Contact Map |
| 1pu6A | 2 | 0.9539 | 99.9 | 0.357 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)