| 4he6A |
| ID: | 1491917802 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 89 (85) | ||
| Sequences: | 970 (728.4) | ||
| Seq/Len: | 11.412 | ||
| Nf(neff/√len): | 79.0 |
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: 11.412).
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 |
| 55_D | 59_N | 4.251 | 1.00 |
| 29_H | 63_A | 2.862 | 1.00 |
| 23_T | 72_K | 2.319 | 1.00 |
| 40_G | 83_N | 2.131 | 1.00 |
| 17_P | 78_P | 1.991 | 1.00 |
| 23_T | 70_I | 1.978 | 1.00 |
| 35_E | 49_V | 1.964 | 1.00 |
| 52_K | 60_E | 1.945 | 1.00 |
| 14_G | 23_T | 1.914 | 1.00 |
| 34_D | 87_K | 1.823 | 1.00 |
| 25_Q | 68_L | 1.748 | 1.00 |
| 52_K | 74_K | 1.730 | 1.00 |
| 80_F | 83_N | 1.636 | 1.00 |
| 10_G | 24_V | 1.600 | 1.00 |
| 30_F | 71_V | 1.593 | 1.00 |
| 42_E | 45_N | 1.550 | 1.00 |
| 14_G | 81_P | 1.525 | 1.00 |
| 55_D | 69_Q | 1.482 | 1.00 |
| 22_A | 73_F | 1.464 | 1.00 |
| 64_A | 71_V | 1.455 | 1.00 |
| 6_R | 88_E | 1.442 | 1.00 |
| 15_Y | 20_G | 1.441 | 1.00 |
| 15_Y | 22_A | 1.418 | 1.00 |
| 21_I | 72_K | 1.401 | 0.99 |
| 48_Q | 76_K | 1.375 | 0.99 |
| 53_I | 61_L | 1.367 | 0.99 |
| 9_A | 36_V | 1.363 | 0.99 |
| 15_Y | 19_T | 1.297 | 0.99 |
| 7_E | 87_K | 1.242 | 0.98 |
| 21_I | 54_W | 1.232 | 0.98 |
| 36_V | 50_I | 1.191 | 0.98 |
| 32_P | 53_I | 1.184 | 0.98 |
| 13_L | 23_T | 1.178 | 0.98 |
| 13_L | 70_I | 1.166 | 0.97 |
| 38_F | 48_Q | 1.163 | 0.97 |
| 31_R | 63_A | 1.140 | 0.97 |
| 26_Q | 66_H | 1.120 | 0.96 |
| 61_L | 69_Q | 1.110 | 0.96 |
| 16_D | 19_T | 1.082 | 0.96 |
| 8_F | 69_Q | 1.081 | 0.95 |
| 55_D | 61_L | 1.073 | 0.95 |
| 38_F | 85_M | 1.070 | 0.95 |
| 13_L | 25_Q | 1.045 | 0.94 |
| 75_V | 79_L | 1.023 | 0.93 |
| 26_Q | 68_L | 1.020 | 0.93 |
| 26_Q | 69_Q | 1.003 | 0.93 |
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 | |
| 4he6A | 1 | 1 | 99.8 | 0.174 | Contact Map |
| 4crnP | 1 | 0.8652 | 50.2 | 0.839 | Contact Map |
| 3avxA | 1 | 0.9663 | 41.2 | 0.847 | Contact Map |
| 1r5bA | 1 | 0.8652 | 40 | 0.849 | Contact Map |
| 1d2eA | 4 | 0.9663 | 36.7 | 0.851 | Contact Map |
| 1s0uA | 1 | 0.8652 | 34.6 | 0.854 | Contact Map |
| 1g7sA | 1 | 0.9663 | 31.3 | 0.857 | Contact Map |
| 1zunB | 1 | 0.9438 | 30.9 | 0.857 | Contact Map |
| 4d61i | 1 | 0.9438 | 29.9 | 0.858 | Contact Map |
| 4rd4A | 1 | 0 | 28 | 0.861 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)