| HR5460A |
| ID: | 1446023057 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 150 (141) | ||
| Sequences: | 503 (317.1) | ||
| Seq/Len: | 3.567 | ||
| Nf(neff/√len): | 26.7 |
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: 3.567).
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 |
| 110_E | 146_R | 4.212 | 1.00 |
| 103_I | 135_F | 3.005 | 1.00 |
| 143_F | 146_R | 2.636 | 1.00 |
| 52_L | 71_Y | 2.510 | 1.00 |
| 31_I | 71_Y | 2.389 | 1.00 |
| 35_E | 74_K | 2.237 | 1.00 |
| 34_V | 48_L | 2.122 | 1.00 |
| 25_G | 29_R | 2.026 | 1.00 |
| 22_D | 67_R | 1.816 | 0.99 |
| 62_Y | 67_R | 1.786 | 0.99 |
| 124_R | 128_N | 1.689 | 0.99 |
| 56_F | 67_R | 1.643 | 0.99 |
| 122_L | 143_F | 1.635 | 0.98 |
| 119_S | 140_Y | 1.575 | 0.98 |
| 139_Q | 142_L | 1.547 | 0.98 |
| 66_P | 98_S | 1.538 | 0.97 |
| 27_W | 52_L | 1.507 | 0.97 |
| 36_E | 74_K | 1.505 | 0.97 |
| 62_Y | 65_D | 1.499 | 0.97 |
| 68_F | 72_C | 1.496 | 0.97 |
| 38_F | 43_E | 1.439 | 0.96 |
| 114_E | 117_H | 1.423 | 0.95 |
| 23_P | 67_R | 1.409 | 0.95 |
| 69_I | 89_L | 1.396 | 0.95 |
| 22_D | 62_Y | 1.362 | 0.94 |
| 125_G | 136_L | 1.344 | 0.93 |
| 34_V | 38_F | 1.327 | 0.93 |
| 31_I | 52_L | 1.296 | 0.92 |
| 76_A | 98_S | 1.291 | 0.91 |
| 53_M | 71_Y | 1.283 | 0.91 |
| 56_F | 62_Y | 1.259 | 0.90 |
| 105_W | 114_E | 1.257 | 0.90 |
| 56_F | 68_F | 1.256 | 0.90 |
| 117_H | 120_A | 1.247 | 0.89 |
| 50_E | 88_F | 1.228 | 0.88 |
| 93_G | 96_T | 1.214 | 0.88 |
| 86_F | 141_R | 1.208 | 0.87 |
| 119_S | 123_Q | 1.194 | 0.86 |
| 12_E | 15_M | 1.181 | 0.86 |
| 84_Q | 121_V | 1.176 | 0.85 |
| 20_G | 27_W | 1.166 | 0.85 |
| 114_E | 142_L | 1.162 | 0.84 |
| 113_G | 137_Q | 1.120 | 0.81 |
| 81_D | 112_Q | 1.086 | 0.78 |
| 69_I | 130_A | 1.085 | 0.78 |
| 22_D | 65_D | 1.083 | 0.78 |
| 15_M | 105_W | 1.081 | 0.78 |
| 35_E | 105_W | 1.075 | 0.77 |
| 126_I | 133_R | 1.071 | 0.77 |
| 56_F | 65_D | 1.065 | 0.76 |
| 65_D | 118_A | 1.061 | 0.76 |
| 123_Q | 140_Y | 1.054 | 0.75 |
| 21_N | 24_L | 1.048 | 0.75 |
| 73_L | 97_L | 1.038 | 0.74 |
| 21_N | 135_F | 1.037 | 0.74 |
| 129_Q | 137_Q | 1.035 | 0.74 |
| 24_L | 45_L | 1.034 | 0.73 |
| 23_P | 65_D | 1.027 | 0.73 |
| 19_K | 99_S | 1.024 | 0.72 |
| 29_R | 101_L | 1.016 | 0.72 |
| 69_I | 72_C | 1.015 | 0.71 |
| 48_L | 80_S | 1.015 | 0.71 |
| 29_R | 75_F | 1.012 | 0.71 |
| 129_Q | 133_R | 1.011 | 0.71 |
| 105_W | 121_V | 1.005 | 0.70 |
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 | |
| 4a1gA | 4 | 1 | 100 | 0.039 | Contact Map |
| 2wviA | 1 | 0.9533 | 100 | 0.05 | Contact Map |
| 3eslA | 2 | 1 | 100 | 0.05 | Contact Map |
| 4aezC | 3 | 1 | 100 | 0.16 | Contact Map |
| 4b94A | 4 | 0.8467 | 99.8 | 0.589 | Contact Map |
| 4h7yA | 4 | 0.8467 | 99.8 | 0.629 | Contact Map |
| 2ondA | 2 | 0.82 | 97.9 | 0.831 | Contact Map |
| 2ooeA | 1 | 0.8867 | 97.7 | 0.836 | Contact Map |
| 2uy1A | 1 | 0.92 | 95.7 | 0.874 | Contact Map |
| 4e6hA | 1 | 0.9067 | 92.5 | 0.891 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)