| SYNTH235-345 ACT608-702 |
| ID: | 1424264922 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 206 (139) | ||
| Sequences: | 2201 (1199.7) | ||
| Seq/Len: | 15.835 | ||
| Nf(neff/√len): | 101.8 |
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: 15.835).
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 |
| 35_D | 38_T | 2.867 | 1.00 |
| 34_N | 91_E | 2.058 | 1.00 |
| 32_I | 91_E | 1.845 | 1.00 |
| 43_L | 47_H | 1.799 | 1.00 |
| 47_H | 57_V | 1.789 | 1.00 |
| 134_K | 138_F | 1.743 | 1.00 |
| 18_Q | 23_I | 1.679 | 1.00 |
| 94_D | 98_E | 1.670 | 1.00 |
| 33_V | 42_V | 1.647 | 1.00 |
| 4_K | 12_K | 1.531 | 1.00 |
| 47_H | 74_T | 1.509 | 1.00 |
| 43_L | 72_L | 1.460 | 1.00 |
| 37_D | 41_R | 1.458 | 1.00 |
| 38_T | 41_R | 1.419 | 1.00 |
| 40_Y | 62_A | 1.417 | 1.00 |
| 43_L | 74_T | 1.403 | 0.99 |
| 131_T | 139_N | 1.396 | 0.99 |
| 105_W | 108_K | 1.388 | 0.99 |
| 104_H | 107_Y | 1.377 | 0.99 |
| 43_L | 57_V | 1.339 | 0.99 |
| 70_Q | 96_M | 1.334 | 0.99 |
| 121_W | 139_N | 1.300 | 0.99 |
| 11_C | 15_L | 1.270 | 0.99 |
| 91_E | 95_Q | 1.266 | 0.99 |
| 122_D | 139_N | 1.263 | 0.99 |
| 131_T | 138_F | 1.258 | 0.99 |
| 71_S | 89_R | 1.238 | 0.98 |
| 42_V | 88_I | 1.234 | 0.98 |
| 40_Y | 59_D | 1.231 | 0.98 |
| 40_Y | 44_G | 1.229 | 0.98 |
| 126_A | 130_I | 1.220 | 0.98 |
| 53_R | 57_V | 1.202 | 0.98 |
| 126_A | 133_I | 1.198 | 0.98 |
| 12_K | 85_E | 1.165 | 0.97 |
| 126_A | 132_E | 1.163 | 0.97 |
| 56_R | 75_S | 1.156 | 0.97 |
| 131_T | 136_E | 1.146 | 0.97 |
| 44_G | 47_H | 1.109 | 0.96 |
| 76_M | 86_V | 1.101 | 0.96 |
| 12_K | 25_D | 1.100 | 0.96 |
| 30_R | 89_R | 1.098 | 0.96 |
| 10_Y | 14_V | 1.089 | 0.96 |
| 34_N | 38_T | 1.080 | 0.95 |
| 57_V | 74_T | 1.079 | 0.95 |
| 53_R | 77_I | 1.078 | 0.95 |
| 122_D | 125_T | 1.066 | 0.95 |
| 12_K | 30_R | 1.061 | 0.95 |
| 100_G | 103_A | 1.061 | 0.95 |
| 119_V | 133_I | 1.060 | 0.95 |
| 42_V | 45_Q | 1.051 | 0.94 |
| 115_K | 139_N | 1.049 | 0.94 |
| 7_Y | 10_Y | 1.047 | 0.94 |
| 46_M | 76_M | 1.041 | 0.94 |
| 60_Y | 65_K | 1.033 | 0.94 |
| 125_T | 128_E | 1.033 | 0.94 |
| 30_R | 87_Q | 1.029 | 0.94 |
| 102_A | 107_Y | 1.020 | 0.93 |
| 115_K | 122_D | 1.020 | 0.93 |
| 128_E | 136_E | 1.017 | 0.93 |
| 9_I | 26_I | 1.013 | 0.93 |
| 9_I | 23_I | 1.011 | 0.93 |
| 128_E | 138_F | 1.009 | 0.93 |
| 135_V | 139_N | 1.008 | 0.93 |
| 119_V | 139_N | 1.002 | 0.92 |
| 132_E | 136_E | 1.002 | 0.92 |
| 130_I | 134_K | 1.000 | 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 | |
| 1vj7A | 2 | 0.5291 | 100 | 0.332 | Contact Map |
| 3l9dA | 2 | 0.6893 | 100 | 0.404 | Contact Map |
| 2be3A | 2 | 0.699 | 100 | 0.418 | Contact Map |
| 1y7pA | 3 | 0.3835 | 98.8 | 0.829 | Contact Map |
| 2ko1A | 2 | 0.3883 | 98.7 | 0.833 | Contact Map |
| 2lvwA | 2 | 0.4078 | 98.6 | 0.842 | Contact Map |
| 2pc6A | 4 | 0.3786 | 98.5 | 0.845 | Contact Map |
| 2f1fA | 2 | 0.3738 | 98.5 | 0.845 | Contact Map |
| 2fgcA | 1 | 0.3786 | 98.5 | 0.846 | Contact Map |
| 1zpvA | 3 | 0.3835 | 98.1 | 0.862 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)