| apo_lfabp |
| ID: | 1405071726 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 127 (125) | ||
| Sequences: | 712 (437.2) | ||
| Seq/Len: | 5.696 | ||
| Nf(neff/√len): | 39.1 |
HHblits Results: (2013_03)
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: 5.696).
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 |
| 68_E | 80_K | 2.876 | 1.00 |
| 64_T | 67_E | 2.739 | 1.00 |
| 70_E | 80_K | 2.384 | 1.00 |
| 7_Y | 104_F | 2.314 | 1.00 |
| 90_K | 103_E | 2.301 | 1.00 |
| 47_K | 62_E | 2.202 | 1.00 |
| 46_K | 64_T | 2.045 | 1.00 |
| 73_T | 77_E | 1.922 | 1.00 |
| 101_V | 114_T | 1.876 | 1.00 |
| 47_K | 64_T | 1.827 | 1.00 |
| 51_T | 60_H | 1.817 | 1.00 |
| 81_A | 93_T | 1.767 | 1.00 |
| 85_M | 91_M | 1.765 | 1.00 |
| 25_P | 28_L | 1.730 | 1.00 |
| 27_D | 31_K | 1.722 | 1.00 |
| 67_E | 87_G | 1.715 | 1.00 |
| 72_E | 78_K | 1.697 | 1.00 |
| 11_S | 123_V | 1.684 | 1.00 |
| 43_H | 48_V | 1.631 | 0.99 |
| 6_K | 40_E | 1.627 | 0.99 |
| 19_M | 32_G | 1.611 | 0.99 |
| 70_E | 78_K | 1.609 | 0.99 |
| 4_S | 43_H | 1.571 | 0.99 |
| 45_G | 66_G | 1.557 | 0.99 |
| 41_I | 50_L | 1.542 | 0.99 |
| 9_V | 12_Q | 1.476 | 0.99 |
| 21_A | 116_G | 1.407 | 0.98 |
| 112_T | 123_V | 1.406 | 0.98 |
| 103_E | 112_T | 1.385 | 0.98 |
| 36_K | 124_S | 1.380 | 0.98 |
| 101_V | 112_T | 1.374 | 0.98 |
| 100_S | 111_N | 1.372 | 0.98 |
| 17_P | 20_K | 1.372 | 0.98 |
| 108_T | 125_K | 1.330 | 0.97 |
| 47_K | 67_E | 1.320 | 0.97 |
| 104_F | 107_D | 1.310 | 0.97 |
| 71_L | 81_A | 1.276 | 0.96 |
| 49_K | 62_E | 1.251 | 0.95 |
| 25_P | 29_I | 1.229 | 0.95 |
| 84_K | 94_T | 1.223 | 0.95 |
| 51_T | 58_V | 1.213 | 0.94 |
| 15_F | 19_M | 1.212 | 0.94 |
| 71_L | 93_T | 1.157 | 0.92 |
| 36_K | 104_F | 1.152 | 0.92 |
| 105_N | 110_T | 1.132 | 0.91 |
| 90_K | 101_V | 1.127 | 0.91 |
| 69_C | 75_T | 1.094 | 0.89 |
| 87_G | 104_F | 1.091 | 0.89 |
| 11_S | 112_T | 1.068 | 0.87 |
| 112_T | 121_K | 1.068 | 0.87 |
| 14_N | 17_P | 1.059 | 0.87 |
| 55_G | 75_T | 1.045 | 0.86 |
| 10_Q | 125_K | 1.022 | 0.84 |
| 121_K | 125_K | 1.004 | 0.83 |
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 | |
| 2f73A | 8 | 1 | 100 | 0.011 | Contact Map |
| 2qo4A | 1 | 0.9843 | 100 | 0.027 | Contact Map |
| 2lbaA | 1 | 0.9843 | 100 | 0.034 | Contact Map |
| 3wbgA | 4 | 0.9921 | 100 | 0.04 | Contact Map |
| 3vg7A | 1 | 1 | 100 | 0.046 | Contact Map |
| 3elxA | 1 | 0.9921 | 100 | 0.048 | Contact Map |
| 1mvgA | 1 | 0.9843 | 100 | 0.048 | Contact Map |
| 1p6pA | 1 | 0.9843 | 100 | 0.048 | Contact Map |
| 3q6lA | 1 | 0.9921 | 100 | 0.051 | Contact Map |
| 4a60A | 1 | 0.9843 | 100 | 0.051 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)