| test2 |
| ID: | 1421599606 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 86 (84) | ||
| Sequences: | 922 (640.7) | ||
| Seq/Len: | 10.976 | ||
| Nf(neff/√len): | 69.9 |
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: 10.976).
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 |
| 48_D | 51_G | 3.480 | 1.00 |
| 59_N | 62_K | 3.422 | 1.00 |
| 38_D | 63_G | 3.231 | 1.00 |
| 43_R | 56_D | 3.000 | 1.00 |
| 2_Q | 70_M | 2.664 | 1.00 |
| 64_T | 72_A | 2.584 | 1.00 |
| 27_I | 77_V | 2.057 | 1.00 |
| 38_D | 62_K | 2.054 | 1.00 |
| 29_S | 61_L | 1.914 | 1.00 |
| 7_K | 11_E | 1.874 | 1.00 |
| 55_W | 59_N | 1.780 | 1.00 |
| 71_K | 75_D | 1.777 | 1.00 |
| 26_F | 76_K | 1.732 | 1.00 |
| 33_Q | 37_G | 1.695 | 1.00 |
| 20_A | 23_E | 1.508 | 1.00 |
| 41_T | 55_W | 1.496 | 1.00 |
| 68_D | 72_A | 1.401 | 0.99 |
| 10_E | 13_K | 1.372 | 0.99 |
| 26_F | 30_H | 1.321 | 0.99 |
| 39_I | 55_W | 1.320 | 0.99 |
| 21_D | 24_M | 1.272 | 0.99 |
| 66_K | 70_M | 1.270 | 0.99 |
| 31_Y | 73_Y | 1.256 | 0.99 |
| 61_L | 64_T | 1.253 | 0.99 |
| 78_E | 81_K | 1.253 | 0.99 |
| 32_K | 73_Y | 1.241 | 0.98 |
| 46_M | 52_K | 1.238 | 0.98 |
| 68_D | 71_K | 1.216 | 0.98 |
| 52_K | 56_D | 1.199 | 0.98 |
| 19_P | 24_M | 1.165 | 0.97 |
| 6_D | 10_E | 1.130 | 0.97 |
| 2_Q | 6_D | 1.100 | 0.96 |
| 3_A | 7_K | 1.099 | 0.96 |
| 11_E | 81_K | 1.087 | 0.96 |
| 23_E | 76_K | 1.083 | 0.96 |
| 4_E | 8_A | 1.082 | 0.96 |
| 15_L | 19_P | 1.070 | 0.95 |
| 65_S | 68_D | 1.064 | 0.95 |
| 36_V | 40_N | 1.059 | 0.95 |
| 25_L | 28_Y | 1.055 | 0.95 |
| 26_F | 60_E | 1.049 | 0.94 |
| 49_F | 52_K | 1.019 | 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 | |
| 2cb8A | 2 | 1 | 100 | 0.007 | Contact Map |
| 3epyA | 2 | 1 | 100 | 0.016 | Contact Map |
| 3flvA | 2 | 1 | 100 | 0.018 | Contact Map |
| 2lbbA | 1 | 1 | 100 | 0.026 | Contact Map |
| 3fp5A | 1 | 1 | 100 | 0.033 | Contact Map |
| 1st7A | 1 | 1 | 100 | 0.037 | Contact Map |
| 2copA | 1 | 1 | 100 | 0.039 | Contact Map |
| 1hbkA | 1 | 1 | 100 | 0.041 | Contact Map |
| 2cquA | 1 | 1 | 100 | 0.042 | Contact Map |
| 2wh5A | 6 | 0.9884 | 100 | 0.063 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)