| xpb_ntd |
| ID: | 1444655635 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 130 (130) | ||
| Sequences: | 991 (617) | ||
| Seq/Len: | 7.623 | ||
| Nf(neff/√len): | 54.1 |
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: 7.623).
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 | 2.955 | 1.00 |
| 67_T | 86_I | 2.412 | 1.00 |
| 66_I | 90_T | 2.275 | 1.00 |
| 35_E | 49_T | 2.176 | 1.00 |
| 71_R | 83_M | 2.088 | 1.00 |
| 62_Q | 65_D | 2.028 | 1.00 |
| 16_L | 22_V | 1.966 | 1.00 |
| 53_L | 66_I | 1.815 | 1.00 |
| 67_T | 87_K | 1.796 | 1.00 |
| 67_T | 83_M | 1.745 | 1.00 |
| 35_E | 55_A | 1.740 | 1.00 |
| 83_M | 87_K | 1.584 | 1.00 |
| 64_S | 87_K | 1.574 | 1.00 |
| 68_E | 72_K | 1.549 | 1.00 |
| 116_Q | 120_Q | 1.518 | 1.00 |
| 80_D | 84_Q | 1.513 | 0.99 |
| 109_S | 115_I | 1.504 | 0.99 |
| 37_V | 47_K | 1.453 | 0.99 |
| 68_E | 86_I | 1.422 | 0.99 |
| 74_S | 83_M | 1.366 | 0.99 |
| 14_I | 70_L | 1.362 | 0.99 |
| 34_A | 46_Y | 1.356 | 0.99 |
| 69_Y | 73_L | 1.347 | 0.99 |
| 13_H | 20_S | 1.345 | 0.99 |
| 8_V | 14_I | 1.302 | 0.98 |
| 33_I | 66_I | 1.299 | 0.98 |
| 35_E | 44_H | 1.285 | 0.98 |
| 14_I | 30_L | 1.280 | 0.98 |
| 56_A | 66_I | 1.279 | 0.98 |
| 17_E | 20_S | 1.270 | 0.98 |
| 36_P | 44_H | 1.269 | 0.98 |
| 1_H | 4_R | 1.261 | 0.98 |
| 49_T | 53_L | 1.242 | 0.97 |
| 116_Q | 126_E | 1.232 | 0.97 |
| 17_E | 75_K | 1.204 | 0.96 |
| 2_T | 43_V | 1.203 | 0.96 |
| 48_L | 78_V | 1.191 | 0.96 |
| 79_P | 82_I | 1.183 | 0.96 |
| 81_G | 102_H | 1.168 | 0.96 |
| 118_L | 121_D | 1.150 | 0.95 |
| 99_V | 106_F | 1.126 | 0.94 |
| 115_I | 128_R | 1.124 | 0.94 |
| 78_V | 83_M | 1.119 | 0.94 |
| 33_I | 70_L | 1.114 | 0.94 |
| 50_A | 89_C | 1.105 | 0.94 |
| 45_E | 55_A | 1.103 | 0.94 |
| 84_Q | 88_L | 1.098 | 0.93 |
| 48_L | 81_G | 1.097 | 0.93 |
| 13_H | 88_L | 1.096 | 0.93 |
| 58_S | 93_Y | 1.089 | 0.93 |
| 15_F | 36_P | 1.083 | 0.93 |
| 8_V | 78_V | 1.082 | 0.93 |
| 22_V | 69_Y | 1.073 | 0.92 |
| 63_T | 90_T | 1.072 | 0.92 |
| 2_T | 80_D | 1.070 | 0.92 |
| 54_Y | 94_G | 1.068 | 0.92 |
| 6_L | 16_L | 1.058 | 0.92 |
| 56_A | 59_V | 1.055 | 0.91 |
| 30_L | 71_R | 1.051 | 0.91 |
| 7_W | 15_F | 1.047 | 0.91 |
| 8_V | 48_L | 1.046 | 0.91 |
| 117_H | 122_P | 1.046 | 0.91 |
| 44_H | 75_K | 1.045 | 0.91 |
| 10_P | 41_T | 1.029 | 0.90 |
| 11_D | 37_V | 1.017 | 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 | 0.4077 | 85.1 | 0.843 | Contact Map |
| 3dgpA | 1 | 0.2846 | 67.1 | 0.866 | Contact Map |
| 3a1yG | 1 | 0.6769 | 17.7 | 0.904 | Contact Map |
| 3m1tA | 1 | 0.4154 | 13.6 | 0.909 | Contact Map |
| 2nn6H | 1 | 0.6846 | 12.9 | 0.91 | Contact Map |
| 1vq8G | 1 | 0 | 12.4 | 0.911 | Contact Map |
| 3j3bq | 1 | 0.9538 | 10 | 0.914 | Contact Map |
| 3j21k | 1 | 0.5077 | 8.5 | 0.917 | Contact Map |
| 4ifdH | 1 | 0.6308 | 8.4 | 0.917 | Contact Map |
| 3l15A | 2 | 0.3769 | 7.4 | 0.919 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)