| PTE2 |
| ID: | 1451219874 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 102 (92) | ||
| Sequences: | 510 (329.9) | ||
| Seq/Len: | 5.543 | ||
| Nf(neff/√len): | 34.4 |
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: 5.543).
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 |
| 89_R | 95_Q | 3.378 | 1.00 |
| 46_K | 100_G | 2.738 | 1.00 |
| 45_M | 100_G | 2.647 | 1.00 |
| 50_V | 101_I | 2.273 | 1.00 |
| 94_P | 97_T | 2.269 | 1.00 |
| 7_I | 84_V | 2.077 | 1.00 |
| 38_A | 41_D | 2.013 | 1.00 |
| 38_A | 42_Q | 2.012 | 1.00 |
| 95_Q | 99_A | 1.926 | 1.00 |
| 1_L | 49_L | 1.846 | 1.00 |
| 5_D | 53_D | 1.776 | 1.00 |
| 85_I | 89_R | 1.769 | 1.00 |
| 88_L | 93_V | 1.765 | 1.00 |
| 40_I | 101_I | 1.700 | 1.00 |
| 78_A | 82_L | 1.668 | 1.00 |
| 44_Y | 48_I | 1.487 | 0.99 |
| 6_H | 55_L | 1.415 | 0.98 |
| 37_K | 41_D | 1.411 | 0.98 |
| 40_I | 45_M | 1.386 | 0.98 |
| 5_D | 43_G | 1.377 | 0.98 |
| 33_A | 91_K | 1.305 | 0.96 |
| 1_L | 47_Q | 1.272 | 0.96 |
| 4_L | 39_L | 1.254 | 0.95 |
| 37_K | 40_I | 1.235 | 0.95 |
| 54_W | 76_G | 1.217 | 0.94 |
| 57_G | 76_G | 1.205 | 0.94 |
| 37_K | 93_V | 1.159 | 0.92 |
| 1_L | 37_K | 1.103 | 0.89 |
| 54_W | 77_M | 1.103 | 0.89 |
| 40_I | 93_V | 1.094 | 0.89 |
| 40_I | 97_T | 1.094 | 0.89 |
| 34_L | 91_K | 1.079 | 0.88 |
| 43_G | 53_D | 1.072 | 0.87 |
| 33_A | 87_F | 1.061 | 0.86 |
| 49_L | 101_I | 1.060 | 0.86 |
| 45_M | 97_T | 1.049 | 0.86 |
| 7_I | 79_F | 1.048 | 0.85 |
| 73_N | 76_G | 1.044 | 0.85 |
| 69_M | 72_V | 1.033 | 0.84 |
| 8_P | 51_S | 1.025 | 0.84 |
| 81_P | 85_I | 1.023 | 0.84 |
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 | |
| 3k2gA | 4 | 0.8333 | 98.9 | 0.565 | Contact Map |
| 3rhgA | 1 | 0.8431 | 98.8 | 0.582 | Contact Map |
| 3pnzA | 6 | 0.7647 | 97.7 | 0.695 | Contact Map |
| 3gtxA | 1 | 0.8824 | 97.2 | 0.717 | Contact Map |
| 4kezA | 4 | 0.8431 | 97 | 0.728 | Contact Map |
| 3tn4A | 2 | 0.8824 | 96.9 | 0.729 | Contact Map |
| 3ovgA | 6 | 0.8137 | 96.8 | 0.734 | Contact Map |
| 1bf6A | 2 | 0.7745 | 96.8 | 0.734 | Contact Map |
| 4if2A | 1 | 0.8431 | 96.8 | 0.736 | Contact Map |
| 2ob3A | 2 | 0.9216 | 96.6 | 0.741 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)