| RGS |
| ID: | 1402294649 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 124 (121) | ||
| Sequences: | 1852 (1199.3) | ||
| Seq/Len: | 15.306 | ||
| Nf(neff/√len): | 109.0 |
Jackhmmer Results: (2014_04_16)
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: 15.306).
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 |
| 30_F | 34_C | 2.861 | 1.00 |
| 33_A | 61_Y | 2.477 | 1.00 |
| 18_F | 113_S | 2.404 | 1.00 |
| 31_W | 99_Q | 2.256 | 1.00 |
| 20_K | 25_A | 2.120 | 1.00 |
| 37_F | 54_A | 2.050 | 1.00 |
| 80_F | 97_Q | 1.980 | 1.00 |
| 35_T | 99_Q | 1.927 | 1.00 |
| 35_T | 38_R | 1.887 | 1.00 |
| 5_L | 111_Y | 1.862 | 1.00 |
| 106_M | 110_T | 1.855 | 1.00 |
| 37_F | 50_R | 1.852 | 1.00 |
| 26_D | 72_Q | 1.782 | 1.00 |
| 12_I | 32_F | 1.780 | 1.00 |
| 70_S | 78_K | 1.697 | 1.00 |
| 109_N | 113_S | 1.676 | 1.00 |
| 5_L | 11_G | 1.644 | 1.00 |
| 38_R | 96_D | 1.599 | 1.00 |
| 38_R | 99_Q | 1.533 | 1.00 |
| 22_E | 113_S | 1.512 | 1.00 |
| 30_F | 98_A | 1.500 | 1.00 |
| 36_G | 53_L | 1.492 | 1.00 |
| 31_W | 106_M | 1.431 | 1.00 |
| 23_G | 27_L | 1.429 | 1.00 |
| 16_R | 29_D | 1.416 | 1.00 |
| 24_C | 110_T | 1.375 | 0.99 |
| 62_I | 71_R | 1.356 | 0.99 |
| 16_R | 28_L | 1.325 | 0.99 |
| 62_I | 78_K | 1.312 | 0.99 |
| 54_A | 95_F | 1.302 | 0.99 |
| 80_F | 83_G | 1.301 | 0.99 |
| 31_W | 35_T | 1.299 | 0.99 |
| 77_T | 101_E | 1.288 | 0.99 |
| 74_K | 77_T | 1.285 | 0.99 |
| 19_L | 106_M | 1.283 | 0.99 |
| 19_L | 110_T | 1.250 | 0.99 |
| 21_Q | 119_I | 1.240 | 0.98 |
| 93_A | 96_D | 1.193 | 0.98 |
| 15_F | 19_L | 1.191 | 0.98 |
| 27_L | 105_T | 1.185 | 0.98 |
| 2_L | 6_L | 1.174 | 0.98 |
| 16_R | 25_A | 1.152 | 0.97 |
| 118_D | 122_E | 1.151 | 0.97 |
| 3_H | 103_Q | 1.151 | 0.97 |
| 13_S | 17_T | 1.147 | 0.97 |
| 109_N | 112_P | 1.145 | 0.97 |
| 23_G | 26_D | 1.124 | 0.97 |
| 81_I | 98_A | 1.121 | 0.97 |
| 16_R | 32_F | 1.102 | 0.96 |
| 17_T | 20_K | 1.096 | 0.96 |
| 11_G | 14_L | 1.082 | 0.96 |
| 77_T | 98_A | 1.075 | 0.95 |
| 37_F | 95_F | 1.061 | 0.95 |
| 30_F | 102_I | 1.060 | 0.95 |
| 90_I | 94_M | 1.038 | 0.94 |
| 19_L | 27_L | 1.017 | 0.93 |
| 55_R | 59_R | 1.016 | 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 | |
| 2pbiA | 2 | 0.9355 | 99.9 | 0.129 | Contact Map |
| 1agrE | 2 | 0.9435 | 99.9 | 0.137 | Contact Map |
| 1dk8A | 1 | 0.9919 | 99.9 | 0.14 | Contact Map |
| 4iguA | 2 | 0.9435 | 99.9 | 0.144 | Contact Map |
| 1zv4X | 1 | 0.9355 | 99.9 | 0.144 | Contact Map |
| 2ihdA | 1 | 0.9435 | 99.9 | 0.145 | Contact Map |
| 3c7lA | 2 | 0.9435 | 99.9 | 0.152 | Contact Map |
| 1cmzA | 1 | 0.9435 | 99.9 | 0.153 | Contact Map |
| 2crpA | 1 | 0.9435 | 99.9 | 0.154 | Contact Map |
| 2af0A | 1 | 0.9435 | 99.9 | 0.154 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)