| d4u2nb1 |
| ID: | 1449333868 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 105 (101) | ||
| Sequences: | 9014 (5852.2) | ||
| Seq/Len: | 89.248 | ||
| Nf(neff/√len): | 582.3 |
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: 89.248).
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 |
| 27_T | 34_H | 3.011 | 1.00 |
| 30_V | 70_L | 2.806 | 1.00 |
| 29_V | 59_V | 2.387 | 1.00 |
| 26_C | 37_A | 2.275 | 1.00 |
| 35_F | 67_A | 2.198 | 1.00 |
| 73_V | 101_M | 2.129 | 1.00 |
| 29_V | 34_H | 2.111 | 1.00 |
| 65_S | 95_V | 1.976 | 1.00 |
| 34_H | 59_V | 1.960 | 1.00 |
| 66_N | 91_D | 1.951 | 1.00 |
| 38_H | 78_Y | 1.777 | 1.00 |
| 47_E | 100_Q | 1.753 | 1.00 |
| 73_V | 95_V | 1.742 | 1.00 |
| 33_V | 71_G | 1.724 | 1.00 |
| 29_V | 61_H | 1.708 | 1.00 |
| 27_T | 36_K | 1.702 | 1.00 |
| 33_V | 67_A | 1.649 | 1.00 |
| 28_F | 70_L | 1.600 | 1.00 |
| 77_M | 101_M | 1.588 | 1.00 |
| 35_F | 71_G | 1.588 | 1.00 |
| 22_L | 50_K | 1.574 | 1.00 |
| 45_C | 77_M | 1.532 | 1.00 |
| 65_S | 70_L | 1.460 | 1.00 |
| 28_F | 37_A | 1.452 | 1.00 |
| 71_G | 75_E | 1.409 | 1.00 |
| 48_Y | 99_L | 1.379 | 0.99 |
| 66_N | 69_G | 1.378 | 0.99 |
| 64_I | 98_F | 1.378 | 0.99 |
| 49_F | 53_F | 1.371 | 0.99 |
| 15_N | 18_R | 1.355 | 0.99 |
| 17_Q | 40_A | 1.354 | 0.99 |
| 21_G | 36_K | 1.353 | 0.99 |
| 35_F | 74_L | 1.346 | 0.99 |
| 68_A | 88_N | 1.269 | 0.99 |
| 37_A | 74_L | 1.260 | 0.99 |
| 15_N | 19_Q | 1.218 | 0.98 |
| 69_G | 95_V | 1.197 | 0.98 |
| 22_L | 54_V | 1.193 | 0.98 |
| 51_M | 55_D | 1.184 | 0.98 |
| 80_A | 103_D | 1.147 | 0.97 |
| 69_G | 91_D | 1.142 | 0.97 |
| 27_T | 59_V | 1.111 | 0.96 |
| 7_S | 11_L | 1.105 | 0.96 |
| 10_V | 14_L | 1.098 | 0.96 |
| 72_Q | 92_V | 1.092 | 0.96 |
| 85_S | 88_N | 1.089 | 0.96 |
| 13_Q | 45_C | 1.083 | 0.96 |
| 73_V | 99_L | 1.065 | 0.95 |
| 26_C | 42_L | 1.058 | 0.95 |
| 13_Q | 16_Q | 1.055 | 0.95 |
| 39_K | 43_A | 1.054 | 0.95 |
| 18_R | 75_E | 1.047 | 0.94 |
| 26_C | 53_F | 1.035 | 0.94 |
| 26_C | 60_V | 1.029 | 0.94 |
| 12_E | 16_Q | 1.021 | 0.93 |
| 50_K | 54_V | 1.018 | 0.93 |
| 82_L | 104_I | 1.001 | 0.92 |
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 | |
| 4u2mA | 4 | 1 | 99.8 | 0.041 | Contact Map |
| 4u2nA | 2 | 1 | 99.8 | 0.049 | Contact Map |
| 2q81A | 4 | 1 | 99.8 | 0.066 | Contact Map |
| 3hveA | 1 | 0.9238 | 99.8 | 0.072 | Contact Map |
| 4hxiA | 1 | 0.9524 | 99.8 | 0.076 | Contact Map |
| 1buoA | 1 | 1 | 99.8 | 0.083 | Contact Map |
| 3fkcA | 1 | 1 | 99.8 | 0.085 | Contact Map |
| 2yy9A | 2 | 0.9714 | 99.8 | 0.087 | Contact Map |
| 2ppiA | 1 | 0.981 | 99.7 | 0.091 | Contact Map |
| 3i3nA | 2 | 0.9905 | 99.7 | 0.092 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)