| ntd |
| ID: | 1440024882 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 130 (130) | ||
| Sequences: | 975 (612.5) | ||
| Seq/Len: | 7.500 | ||
| Nf(neff/√len): | 53.7 |
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: 7.500).
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 |
| 14_I | 48_L | 3.242 | 1.00 |
| 67_T | 86_I | 2.376 | 1.00 |
| 66_I | 90_T | 2.323 | 1.00 |
| 35_E | 49_T | 2.289 | 1.00 |
| 71_R | 83_M | 2.045 | 1.00 |
| 62_Q | 65_D | 1.955 | 1.00 |
| 67_T | 87_K | 1.881 | 1.00 |
| 35_E | 55_A | 1.827 | 1.00 |
| 53_L | 66_I | 1.792 | 1.00 |
| 67_T | 83_M | 1.775 | 1.00 |
| 68_E | 72_K | 1.758 | 1.00 |
| 16_L | 22_V | 1.752 | 1.00 |
| 83_M | 87_K | 1.612 | 1.00 |
| 64_S | 87_K | 1.594 | 1.00 |
| 80_D | 84_Q | 1.547 | 1.00 |
| 37_V | 47_K | 1.537 | 1.00 |
| 116_Q | 120_Q | 1.480 | 0.99 |
| 14_I | 30_L | 1.447 | 0.99 |
| 109_S | 115_I | 1.418 | 0.99 |
| 14_I | 70_L | 1.388 | 0.99 |
| 69_Y | 73_L | 1.373 | 0.99 |
| 13_H | 20_S | 1.326 | 0.98 |
| 34_A | 46_Y | 1.315 | 0.98 |
| 33_I | 66_I | 1.308 | 0.98 |
| 56_A | 66_I | 1.305 | 0.98 |
| 8_V | 78_V | 1.283 | 0.98 |
| 35_E | 44_H | 1.280 | 0.98 |
| 99_V | 106_F | 1.276 | 0.98 |
| 48_L | 78_V | 1.265 | 0.98 |
| 1_H | 4_R | 1.264 | 0.97 |
| 36_P | 44_H | 1.258 | 0.97 |
| 17_E | 20_S | 1.247 | 0.97 |
| 74_S | 83_M | 1.231 | 0.97 |
| 68_E | 86_I | 1.217 | 0.97 |
| 79_P | 82_I | 1.179 | 0.96 |
| 15_F | 36_P | 1.175 | 0.96 |
| 49_T | 53_L | 1.152 | 0.95 |
| 48_L | 81_G | 1.152 | 0.95 |
| 58_S | 93_Y | 1.150 | 0.95 |
| 116_Q | 126_E | 1.139 | 0.95 |
| 13_H | 88_L | 1.135 | 0.94 |
| 84_Q | 88_L | 1.124 | 0.94 |
| 56_A | 59_V | 1.121 | 0.94 |
| 81_G | 102_H | 1.113 | 0.94 |
| 8_V | 14_I | 1.106 | 0.93 |
| 54_Y | 94_G | 1.100 | 0.93 |
| 34_A | 47_K | 1.095 | 0.93 |
| 50_A | 89_C | 1.090 | 0.93 |
| 17_E | 75_K | 1.085 | 0.93 |
| 2_T | 80_D | 1.080 | 0.92 |
| 2_T | 43_V | 1.065 | 0.92 |
| 44_H | 75_K | 1.060 | 0.91 |
| 22_V | 69_Y | 1.046 | 0.91 |
| 118_L | 121_D | 1.033 | 0.90 |
| 30_L | 71_R | 1.033 | 0.90 |
| 78_V | 83_M | 1.014 | 0.89 |
| 45_E | 55_A | 1.011 | 0.89 |
| 53_L | 108_E | 1.010 | 0.89 |
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 | |
| 3domA | 2 | 0.3923 | 83.8 | 0.842 | Contact Map |
| 3dgpA | 1 | 0.2769 | 67.9 | 0.862 | Contact Map |
| 3a1yG | 1 | 0.6769 | 13.2 | 0.908 | Contact Map |
| 1vq8G | 1 | 0 | 9.2 | 0.914 | Contact Map |
| 2nn6H | 1 | 0.6846 | 9.2 | 0.914 | Contact Map |
| 4dn7A | 2 | 0.6615 | 9 | 0.914 | Contact Map |
| 3m1tA | 1 | 0.4154 | 8.6 | 0.915 | Contact Map |
| 2o36A | 1 | 0.6385 | 6.6 | 0.92 | Contact Map |
| 4c0oA | 2 | 0.6615 | 6.2 | 0.92 | Contact Map |
| 3j21k | 1 | 0.5077 | 5.9 | 0.921 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)