| 3zja |
| ID: | 1501760547 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 114 (113) | ||
| Sequences: | 687 (685) | ||
| Seq/Len: | 6.080 | ||
| Nf(neff/√len): | 64.4 |
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: 6.080).
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 |
| 5_V | 8_A | 2.347 | 1.00 |
| 35_L | 99_F | 2.329 | 1.00 |
| 55_M | 79_M | 2.127 | 1.00 |
| 32_A | 65_A | 2.116 | 1.00 |
| 34_E | 100_A | 2.094 | 1.00 |
| 39_T | 98_H | 1.850 | 1.00 |
| 64_P | 67_G | 1.842 | 1.00 |
| 33_D | 101_H | 1.832 | 1.00 |
| 38_V | 97_L | 1.832 | 1.00 |
| 38_V | 47_V | 1.830 | 1.00 |
| 23_L | 71_F | 1.822 | 1.00 |
| 33_D | 102_S | 1.785 | 1.00 |
| 23_L | 78_L | 1.759 | 1.00 |
| 41_E | 94_A | 1.756 | 1.00 |
| 46_T | 57_E | 1.747 | 1.00 |
| 43_G | 82_K | 1.687 | 1.00 |
| 32_A | 62_E | 1.649 | 1.00 |
| 21_G | 109_L | 1.635 | 1.00 |
| 37_S | 98_H | 1.597 | 0.99 |
| 46_T | 81_E | 1.583 | 0.99 |
| 10_I | 93_V | 1.550 | 0.99 |
| 61_I | 69_L | 1.515 | 0.99 |
| 6_D | 26_T | 1.491 | 0.99 |
| 34_E | 60_R | 1.459 | 0.99 |
| 24_T | 70_V | 1.451 | 0.99 |
| 95_V | 109_L | 1.438 | 0.99 |
| 38_V | 45_V | 1.429 | 0.99 |
| 33_D | 103_D | 1.405 | 0.98 |
| 50_T | 53_G | 1.367 | 0.98 |
| 5_V | 23_L | 1.324 | 0.97 |
| 21_G | 80_F | 1.324 | 0.97 |
| 47_V | 61_I | 1.311 | 0.97 |
| 69_L | 76_N | 1.308 | 0.97 |
| 10_I | 21_G | 1.291 | 0.97 |
| 48_H | 77_H | 1.275 | 0.96 |
| 80_F | 95_V | 1.266 | 0.96 |
| 55_M | 77_H | 1.264 | 0.96 |
| 10_I | 19_A | 1.260 | 0.96 |
| 8_A | 109_L | 1.236 | 0.96 |
| 40_S | 80_F | 1.222 | 0.95 |
| 25_I | 91_Q | 1.215 | 0.95 |
| 63_V | 67_G | 1.177 | 0.94 |
| 100_A | 103_D | 1.157 | 0.93 |
| 48_H | 79_M | 1.145 | 0.92 |
| 98_H | 104_P | 1.136 | 0.92 |
| 22_F | 73_S | 1.131 | 0.92 |
| 44_E | 81_E | 1.115 | 0.91 |
| 20_A | 79_M | 1.115 | 0.91 |
| 33_D | 100_A | 1.114 | 0.91 |
| 94_A | 108_K | 1.103 | 0.91 |
| 21_G | 95_V | 1.089 | 0.90 |
| 87_P | 111_V | 1.076 | 0.89 |
| 3_L | 25_I | 1.068 | 0.89 |
| 21_G | 78_L | 1.065 | 0.88 |
| 92_S | 108_K | 1.060 | 0.88 |
| 8_A | 23_L | 1.057 | 0.88 |
| 49_E | 56_K | 1.044 | 0.87 |
| 9_Y | 110_P | 1.039 | 0.87 |
| 26_T | 68_Q | 1.027 | 0.86 |
| 19_A | 83_L | 1.024 | 0.86 |
| 34_E | 62_E | 1.022 | 0.85 |
| 2_E | 29_G | 1.018 | 0.85 |
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 | |
| 3zjaA | 1 | 1 | 100 | -0.03 | Contact Map |
| 1x9lA | 1 | 1 | 99.9 | 0.03 | Contact Map |
| 2k6wA | 1 | 0.9737 | 99.9 | 0.069 | Contact Map |
| 1yewA | 3 | 0.8684 | 75.9 | 0.832 | Contact Map |
| 4phzA | 3 | 0.8596 | 74.3 | 0.835 | Contact Map |
| 2x3cA | 1 | 0.7982 | 49.3 | 0.859 | Contact Map |
| 3isyA | 1 | 0.8684 | 34.3 | 0.871 | Contact Map |
| 3fsaA | 1 | 0.6053 | 29.5 | 0.876 | Contact Map |
| 4ep8B | 1 | 0.8246 | 27.4 | 0.878 | Contact Map |
| 1ufgA | 1 | 0.8772 | 26 | 0.879 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)