| hrd3_262-402 |
| ID: | 1472000616 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 141 (124) | ||
| Sequences: | 468 (357.8) | ||
| Seq/Len: | 3.774 | ||
| Nf(neff/√len): | 32.1 |
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: 3.774).
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 |
| 120_F | 137_L | 2.261 | 1.00 |
| 67_N | 118_M | 2.138 | 1.00 |
| 69_Y | 86_L | 2.137 | 1.00 |
| 81_R | 84_N | 2.104 | 1.00 |
| 132_M | 135_E | 1.876 | 1.00 |
| 98_D | 106_F | 1.870 | 1.00 |
| 51_E | 60_R | 1.793 | 0.99 |
| 61_I | 92_E | 1.770 | 0.99 |
| 87_E | 91_K | 1.733 | 0.99 |
| 101_D | 138_T | 1.689 | 0.99 |
| 76_S | 126_S | 1.681 | 0.99 |
| 127_K | 130_I | 1.598 | 0.98 |
| 50_D | 88_L | 1.577 | 0.98 |
| 52_D | 90_Y | 1.564 | 0.98 |
| 61_I | 112_L | 1.525 | 0.98 |
| 87_E | 101_D | 1.500 | 0.97 |
| 88_L | 102_P | 1.478 | 0.97 |
| 47_D | 85_L | 1.468 | 0.97 |
| 61_I | 98_D | 1.468 | 0.97 |
| 52_D | 61_I | 1.468 | 0.97 |
| 43_N | 46_G | 1.466 | 0.97 |
| 37_F | 48_E | 1.435 | 0.96 |
| 85_L | 88_L | 1.395 | 0.95 |
| 32_M | 36_A | 1.370 | 0.95 |
| 49_D | 101_D | 1.368 | 0.95 |
| 104_Q | 136_I | 1.363 | 0.94 |
| 50_D | 102_P | 1.342 | 0.94 |
| 60_R | 111_C | 1.314 | 0.93 |
| 104_Q | 112_L | 1.298 | 0.92 |
| 85_L | 136_I | 1.291 | 0.92 |
| 52_D | 104_Q | 1.284 | 0.92 |
| 101_D | 105_V | 1.272 | 0.91 |
| 41_D | 100_L | 1.267 | 0.91 |
| 116_G | 125_S | 1.247 | 0.90 |
| 61_I | 104_Q | 1.238 | 0.90 |
| 53_A | 105_V | 1.200 | 0.88 |
| 44_I | 48_E | 1.197 | 0.88 |
| 112_L | 136_I | 1.186 | 0.87 |
| 49_D | 138_T | 1.180 | 0.87 |
| 104_Q | 107_Y | 1.167 | 0.86 |
| 15_P | 18_A | 1.163 | 0.86 |
| 102_P | 139_T | 1.160 | 0.85 |
| 99_N | 108_Y | 1.149 | 0.85 |
| 36_A | 39_G | 1.128 | 0.83 |
| 46_G | 135_E | 1.125 | 0.83 |
| 49_D | 87_E | 1.122 | 0.83 |
| 45_N | 67_N | 1.119 | 0.82 |
| 87_E | 138_T | 1.109 | 0.82 |
| 49_D | 53_A | 1.100 | 0.81 |
| 61_I | 90_Y | 1.093 | 0.80 |
| 103_L | 140_S | 1.092 | 0.80 |
| 47_D | 50_D | 1.090 | 0.80 |
| 90_Y | 98_D | 1.083 | 0.80 |
| 104_Q | 141_L | 1.081 | 0.79 |
| 19_Q | 26_T | 1.077 | 0.79 |
| 84_N | 135_E | 1.071 | 0.78 |
| 128_P | 132_M | 1.060 | 0.77 |
| 45_N | 75_Q | 1.049 | 0.76 |
| 98_D | 112_L | 1.042 | 0.76 |
| 91_K | 105_V | 1.031 | 0.75 |
| 89_T | 103_L | 1.030 | 0.75 |
| 79_C | 100_L | 1.016 | 0.73 |
| 90_Y | 104_Q | 1.015 | 0.73 |
| 22_G | 26_T | 1.012 | 0.73 |
| 37_F | 69_Y | 1.010 | 0.73 |
| 56_R | 140_S | 1.009 | 0.72 |
| 18_A | 26_T | 1.004 | 0.72 |
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 | 0.9007 | 99.8 | 0.499 | Contact Map |
| 1ouvA | 1 | 0.9787 | 99.7 | 0.552 | Contact Map |
| 1klxA | 1 | 0.8652 | 99.6 | 0.58 | Contact Map |
| 3e4bA | 4 | 0.8723 | 99.3 | 0.654 | Contact Map |
| 3rjvA | 1 | 0.9078 | 98.8 | 0.713 | Contact Map |
| 1pc2A | 1 | 0.6809 | 97.2 | 0.811 | Contact Map |
| 1hh8A | 1 | 0.6809 | 96.8 | 0.821 | Contact Map |
| 2vsyA | 2 | 0.6596 | 96.3 | 0.83 | Contact Map |
| 2dbaA | 1 | 0.8298 | 95.9 | 0.837 | Contact Map |
| 4j8fA | 1 | 0.8369 | 95.7 | 0.838 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)