| 1eaza_unfavored |
| ID: | 1492968576 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 103 (103) | ||
| Sequences: | 5171 (1544.7) | ||
| Seq/Len: | 50.204 | ||
| Nf(neff/√len): | 152.2 |
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: 50.204).
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_R | 70_E | 3.389 | 1.00 |
| 96_E | 100_R | 3.326 | 1.00 |
| 59_N | 62_K | 2.971 | 1.00 |
| 12_E | 63_K | 2.847 | 1.00 |
| 21_R | 83_D | 2.809 | 1.00 |
| 52_Q | 74_T | 2.793 | 1.00 |
| 56_E | 60_K | 2.593 | 1.00 |
| 66_P | 81_Q | 2.568 | 1.00 |
| 5_H | 90_A | 2.483 | 1.00 |
| 50_E | 74_T | 2.477 | 1.00 |
| 10_V | 21_R | 2.455 | 1.00 |
| 9_R | 91_D | 2.438 | 1.00 |
| 16_K | 20_E | 2.390 | 1.00 |
| 71_I | 80_V | 2.352 | 1.00 |
| 97_E | 101_A | 2.338 | 1.00 |
| 93_K | 97_E | 2.295 | 1.00 |
| 14_M | 76_R | 2.262 | 1.00 |
| 11_V | 24_W | 2.238 | 1.00 |
| 33_Y | 44_Q | 2.220 | 1.00 |
| 6_S | 23_Y | 2.211 | 1.00 |
| 49_K | 102_Q | 2.175 | 1.00 |
| 3_V | 25_E | 2.046 | 1.00 |
| 67_N | 85_P | 2.027 | 1.00 |
| 29_D | 102_Q | 2.007 | 1.00 |
| 53_R | 103_L | 1.856 | 1.00 |
| 93_K | 96_E | 1.827 | 1.00 |
| 35_R | 39_E | 1.676 | 1.00 |
| 99_I | 103_L | 1.664 | 1.00 |
| 27_R | 30_T | 1.592 | 1.00 |
| 65_R | 81_Q | 1.576 | 1.00 |
| 26_L | 31_I | 1.509 | 1.00 |
| 5_H | 91_D | 1.482 | 1.00 |
| 48_L | 51_V | 1.376 | 0.99 |
| 72_V | 77_V | 1.281 | 0.99 |
| 87_E | 90_A | 1.276 | 0.99 |
| 22_H | 43_L | 1.269 | 0.99 |
| 63_K | 68_L | 1.265 | 0.99 |
| 5_H | 9_R | 1.260 | 0.99 |
| 13_D | 16_K | 1.232 | 0.98 |
| 6_S | 25_E | 1.204 | 0.98 |
| 4_I | 98_A | 1.202 | 0.98 |
| 10_V | 81_Q | 1.184 | 0.98 |
| 47_P | 50_E | 1.171 | 0.98 |
| 4_I | 101_A | 1.157 | 0.97 |
| 4_I | 94_A | 1.120 | 0.96 |
| 86_D | 90_A | 1.104 | 0.96 |
| 10_V | 83_D | 1.088 | 0.96 |
| 83_D | 87_E | 1.084 | 0.96 |
| 69_Y | 91_D | 1.036 | 0.94 |
| 11_V | 33_Y | 1.031 | 0.94 |
| 6_S | 37_K | 1.015 | 0.93 |
| 12_E | 19_W | 1.005 | 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 | |
| 2d9zA | 1 | 1 | 99.7 | 0.67 | Contact Map |
| 2coaA | 1 | 1 | 99.7 | 0.678 | Contact Map |
| 1eazA | 1 | 1 | 99.5 | 0.719 | Contact Map |
| 3ljuX | 1 | 1 | 99.4 | 0.725 | Contact Map |
| 1wi1A | 1 | 0.9903 | 99.4 | 0.728 | Contact Map |
| 1v5pA | 1 | 1 | 99.4 | 0.729 | Contact Map |
| 1u5eA | 2 | 0.9903 | 99.4 | 0.732 | Contact Map |
| 2dkpA | 1 | 0.9903 | 99.4 | 0.732 | Contact Map |
| 1btkA | 2 | 1 | 99.4 | 0.733 | Contact Map |
| 2cocA | 1 | 0.9806 | 99.4 | 0.733 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)