| Ubox_DMS |
| ID: | 1506954968 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 102 (101) | ||
| Sequences: | 726 (450.1) | ||
| Seq/Len: | 7.188 | ||
| Nf(neff/√len): | 44.8 |
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: 7.188).
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 |
| 43_D | 55_R | 3.703 | 1.00 |
| 46_R | 83_V | 3.144 | 1.00 |
| 52_V | 83_V | 3.007 | 1.00 |
| 32_F | 89_Q | 2.963 | 1.00 |
| 42_T | 94_M | 2.118 | 1.00 |
| 46_R | 52_V | 2.096 | 1.00 |
| 92_A | 96_E | 2.043 | 1.00 |
| 84_P | 87_K | 1.910 | 1.00 |
| 88_E | 92_A | 1.834 | 1.00 |
| 77_E | 80_L | 1.772 | 1.00 |
| 13_E | 17_K | 1.698 | 1.00 |
| 49_S | 68_D | 1.634 | 1.00 |
| 86_L | 90_I | 1.611 | 1.00 |
| 87_K | 91_Q | 1.578 | 1.00 |
| 31_E | 89_Q | 1.512 | 0.99 |
| 9_E | 13_E | 1.490 | 0.99 |
| 53_M | 57_I | 1.454 | 0.99 |
| 47_L | 68_D | 1.371 | 0.99 |
| 4_F | 8_A | 1.323 | 0.98 |
| 96_E | 100_S | 1.292 | 0.98 |
| 12_E | 16_A | 1.265 | 0.97 |
| 12_E | 15_V | 1.249 | 0.97 |
| 76_T | 79_M | 1.246 | 0.97 |
| 32_F | 86_L | 1.230 | 0.97 |
| 92_A | 95_R | 1.222 | 0.96 |
| 41_M | 54_D | 1.216 | 0.96 |
| 38_D | 93_W | 1.174 | 0.95 |
| 25_Y | 94_M | 1.163 | 0.95 |
| 1_I | 71_N | 1.143 | 0.94 |
| 85_E | 89_Q | 1.130 | 0.94 |
| 5_K | 9_E | 1.103 | 0.93 |
| 8_A | 11_V | 1.092 | 0.92 |
| 61_H | 72_R | 1.090 | 0.92 |
| 60_R | 73_Q | 1.086 | 0.92 |
| 6_L | 16_A | 1.083 | 0.92 |
| 50_G | 73_Q | 1.077 | 0.92 |
| 3_K | 13_E | 1.074 | 0.92 |
| 75_L | 79_M | 1.068 | 0.91 |
| 59_L | 77_E | 1.066 | 0.91 |
| 46_R | 81_E | 1.052 | 0.90 |
| 57_I | 80_L | 1.039 | 0.90 |
| 6_L | 13_E | 1.033 | 0.89 |
| 33_R | 38_D | 1.025 | 0.89 |
| 36_L | 39_T | 1.017 | 0.88 |
| 32_F | 90_I | 1.016 | 0.88 |
| 47_L | 70_F | 1.002 | 0.87 |
| 13_E | 16_A | 1.002 | 0.87 |
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 | |
| 3m62A | 1 | 0.9902 | 99.9 | 0.222 | Contact Map |
| 4wz3B | 1 | 0.8529 | 99.6 | 0.498 | Contact Map |
| 2kreA | 1 | 0.9804 | 99.5 | 0.52 | Contact Map |
| 2c2lA | 4 | 0.9902 | 99.5 | 0.522 | Contact Map |
| 2f42A | 1 | 0.9706 | 99.5 | 0.538 | Contact Map |
| 2kr4A | 1 | 0.8333 | 99.4 | 0.555 | Contact Map |
| 1wgmA | 1 | 0.9118 | 99.4 | 0.568 | Contact Map |
| 4wz0A | 1 | 0.9412 | 99.3 | 0.571 | Contact Map |
| 3htkC | 1 | 1 | 99.3 | 0.579 | Contact Map |
| 2z6gA | 1 | 0 | 99.2 | 0.597 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)