| hrd3_312-457 |
| ID: | 1472000584 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 146 (123) | ||
| Sequences: | 11963 (9204.1) | ||
| Seq/Len: | 97.260 | ||
| Nf(neff/√len): | 829.9 |
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: 97.260).
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_P | 132_T | 2.143 | 1.00 |
| 62_L | 86_I | 2.085 | 1.00 |
| 100_P | 125_Y | 1.991 | 1.00 |
| 62_L | 94_S | 1.952 | 1.00 |
| 31_R | 34_N | 1.923 | 1.00 |
| 11_I | 35_L | 1.907 | 1.00 |
| 104_A | 126_Y | 1.897 | 1.00 |
| 66_G | 87_L | 1.885 | 1.00 |
| 15_A | 36_L | 1.831 | 1.00 |
| 11_I | 56_F | 1.806 | 1.00 |
| 121_Q | 124_S | 1.782 | 1.00 |
| 82_M | 85_E | 1.747 | 1.00 |
| 108_L | 126_Y | 1.728 | 1.00 |
| 130_M | 140_E | 1.723 | 1.00 |
| 77_K | 80_I | 1.664 | 1.00 |
| 62_L | 89_T | 1.614 | 1.00 |
| 19_Y | 36_L | 1.609 | 1.00 |
| 88_T | 92_E | 1.597 | 1.00 |
| 63_Q | 99_G | 1.560 | 1.00 |
| 70_F | 87_L | 1.537 | 1.00 |
| 101_I | 134_A | 1.507 | 1.00 |
| 14_A | 18_D | 1.490 | 1.00 |
| 37_E | 41_K | 1.473 | 1.00 |
| 127_M | 131_K | 1.459 | 1.00 |
| 11_I | 38_L | 1.456 | 1.00 |
| 90_S | 99_G | 1.452 | 1.00 |
| 63_Q | 102_G | 1.444 | 1.00 |
| 123_I | 127_M | 1.442 | 1.00 |
| 12_Y | 58_Y | 1.440 | 1.00 |
| 100_P | 128_K | 1.431 | 1.00 |
| 63_Q | 96_R | 1.401 | 0.99 |
| 33_K | 75_S | 1.400 | 0.99 |
| 84_E | 88_T | 1.344 | 0.99 |
| 101_I | 142_Q | 1.335 | 0.99 |
| 39_T | 61_C | 1.317 | 0.99 |
| 84_E | 115_I | 1.315 | 0.99 |
| 91_L | 100_P | 1.304 | 0.99 |
| 141_F | 144_S | 1.284 | 0.99 |
| 84_E | 103_R | 1.270 | 0.99 |
| 123_I | 143_L | 1.265 | 0.99 |
| 33_K | 37_E | 1.258 | 0.99 |
| 85_E | 89_T | 1.255 | 0.99 |
| 129_A | 137_G | 1.243 | 0.98 |
| 12_Y | 61_C | 1.227 | 0.98 |
| 33_K | 65_L | 1.222 | 0.98 |
| 125_Y | 128_K | 1.222 | 0.98 |
| 40_Y | 62_L | 1.218 | 0.98 |
| 122_A | 126_Y | 1.203 | 0.98 |
| 108_L | 122_A | 1.203 | 0.98 |
| 103_R | 107_D | 1.185 | 0.98 |
| 65_L | 69_Y | 1.177 | 0.98 |
| 101_I | 137_G | 1.174 | 0.98 |
| 80_I | 113_Q | 1.148 | 0.97 |
| 32_A | 36_L | 1.145 | 0.97 |
| 29_C | 73_E | 1.119 | 0.96 |
| 118_N | 121_Q | 1.110 | 0.96 |
| 28_N | 31_R | 1.105 | 0.96 |
| 60_R | 96_R | 1.101 | 0.96 |
| 12_Y | 64_L | 1.078 | 0.95 |
| 33_K | 68_M | 1.077 | 0.95 |
| 35_L | 38_L | 1.072 | 0.95 |
| 84_E | 106_I | 1.071 | 0.95 |
| 35_L | 39_T | 1.051 | 0.94 |
| 78_P | 82_M | 1.049 | 0.94 |
| 97_A | 134_A | 1.025 | 0.93 |
| 127_M | 143_L | 1.021 | 0.93 |
| 16_L | 19_Y | 1.020 | 0.93 |
| 69_Y | 75_S | 1.013 | 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 | |
| 4bwrA | 1 | 0.8562 | 99.8 | 0.218 | Contact Map |
| 1ouvA | 1 | 0.8562 | 99.6 | 0.295 | Contact Map |
| 1klxA | 1 | 0.7808 | 99.5 | 0.356 | Contact Map |
| 3e4bA | 4 | 0.8493 | 99.1 | 0.489 | Contact Map |
| 3rjvA | 1 | 0.8767 | 98.6 | 0.564 | Contact Map |
| 4gywA | 2 | 0.774 | 96.2 | 0.725 | Contact Map |
| 2pziA | 2 | 0.7808 | 96 | 0.729 | Contact Map |
| 4j8fA | 1 | 0.7808 | 95.9 | 0.731 | Contact Map |
| 1hh8A | 1 | 0.7466 | 95.4 | 0.74 | Contact Map |
| 1na0A | 2 | 0.7534 | 95.4 | 0.74 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)