| hrd3_312-442 |
| ID: | 1472000565 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 131 (109) | ||
| Sequences: | 12861 (10007.1) | ||
| Seq/Len: | 117.991 | ||
| Nf(neff/√len): | 958.5 |
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: 117.991).
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 |
| 62_L | 86_I | 2.222 | 1.00 |
| 66_G | 87_L | 2.115 | 1.00 |
| 11_I | 35_L | 2.099 | 1.00 |
| 100_P | 125_Y | 2.027 | 1.00 |
| 62_L | 94_S | 1.974 | 1.00 |
| 104_A | 126_Y | 1.927 | 1.00 |
| 15_A | 36_L | 1.762 | 1.00 |
| 31_R | 34_N | 1.749 | 1.00 |
| 77_K | 80_I | 1.704 | 1.00 |
| 11_I | 56_F | 1.670 | 1.00 |
| 121_Q | 124_S | 1.658 | 1.00 |
| 108_L | 126_Y | 1.647 | 1.00 |
| 11_I | 38_L | 1.638 | 1.00 |
| 19_Y | 36_L | 1.623 | 1.00 |
| 82_M | 85_E | 1.616 | 1.00 |
| 63_Q | 96_R | 1.614 | 1.00 |
| 63_Q | 99_G | 1.511 | 1.00 |
| 84_E | 88_T | 1.510 | 1.00 |
| 88_T | 92_E | 1.507 | 1.00 |
| 14_A | 18_D | 1.490 | 1.00 |
| 90_S | 99_G | 1.489 | 1.00 |
| 123_I | 127_M | 1.486 | 1.00 |
| 91_L | 100_P | 1.485 | 1.00 |
| 33_K | 75_S | 1.467 | 1.00 |
| 62_L | 89_T | 1.452 | 1.00 |
| 70_F | 87_L | 1.451 | 1.00 |
| 100_P | 128_K | 1.449 | 1.00 |
| 33_K | 37_E | 1.433 | 1.00 |
| 37_E | 41_K | 1.398 | 0.99 |
| 127_M | 131_K | 1.362 | 0.99 |
| 39_T | 61_C | 1.349 | 0.99 |
| 84_E | 115_I | 1.349 | 0.99 |
| 33_K | 65_L | 1.309 | 0.99 |
| 122_A | 126_Y | 1.251 | 0.99 |
| 103_R | 107_D | 1.249 | 0.99 |
| 40_Y | 62_L | 1.248 | 0.99 |
| 12_Y | 58_Y | 1.237 | 0.98 |
| 80_I | 113_Q | 1.227 | 0.98 |
| 28_N | 31_R | 1.223 | 0.98 |
| 65_L | 69_Y | 1.223 | 0.98 |
| 85_E | 89_T | 1.222 | 0.98 |
| 84_E | 103_R | 1.219 | 0.98 |
| 12_Y | 61_C | 1.216 | 0.98 |
| 63_Q | 102_G | 1.196 | 0.98 |
| 70_F | 83_A | 1.173 | 0.98 |
| 125_Y | 128_K | 1.148 | 0.97 |
| 32_A | 36_L | 1.138 | 0.97 |
| 78_P | 82_M | 1.134 | 0.97 |
| 59_V | 96_R | 1.129 | 0.97 |
| 108_L | 122_A | 1.115 | 0.96 |
| 35_L | 39_T | 1.104 | 0.96 |
| 34_N | 38_L | 1.081 | 0.95 |
| 107_D | 121_Q | 1.059 | 0.95 |
| 60_R | 96_R | 1.059 | 0.95 |
| 124_S | 128_K | 1.046 | 0.94 |
| 108_L | 119_I | 1.043 | 0.94 |
| 84_E | 106_I | 1.042 | 0.94 |
| 83_A | 87_L | 1.035 | 0.94 |
| 118_N | 121_Q | 1.025 | 0.93 |
| 69_Y | 75_S | 1.014 | 0.93 |
| 29_C | 73_E | 1.012 | 0.93 |
| 35_L | 38_L | 1.009 | 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 | 0.8473 | 99.7 | 0.138 | Contact Map |
| 1ouvA | 1 | 0.8473 | 99.5 | 0.228 | Contact Map |
| 1klxA | 1 | 0.8015 | 99.3 | 0.309 | Contact Map |
| 3e4bA | 4 | 0.8397 | 98.9 | 0.43 | Contact Map |
| 3rjvA | 1 | 0.8397 | 98.4 | 0.523 | Contact Map |
| 3u64A | 1 | 0.855 | 95.9 | 0.683 | Contact Map |
| 4j8fA | 1 | 0.7786 | 95.7 | 0.688 | Contact Map |
| 4gywA | 2 | 0.7557 | 95.7 | 0.688 | Contact Map |
| 1hh8A | 1 | 0.7786 | 95.5 | 0.692 | Contact Map |
| 2pziA | 2 | 0.771 | 95.4 | 0.693 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)