| test |
| ID: | 1498578189 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 104 (104) | ||
| Sequences: | 8277 (6485.5) | ||
| Seq/Len: | 79.587 | ||
| Nf(neff/√len): | 636.0 |
HHblits Results: (2016_02)
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: 79.587).
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 |
| 82_C | 95_H | 4.370 | 1.00 |
| 54_L | 83_A | 3.484 | 1.00 |
| 19_Q | 28_D | 3.225 | 1.00 |
| 21_F | 101_W | 2.563 | 1.00 |
| 54_L | 64_W | 2.312 | 1.00 |
| 4_K | 104_S | 2.197 | 1.00 |
| 13_K | 17_S | 2.197 | 1.00 |
| 84_Y | 99_R | 2.142 | 1.00 |
| 35_F | 39_N | 2.079 | 1.00 |
| 84_Y | 91_S | 1.984 | 1.00 |
| 13_K | 21_F | 1.977 | 1.00 |
| 21_F | 25_Q | 1.976 | 1.00 |
| 14_N | 17_S | 1.965 | 1.00 |
| 38_L | 90_A | 1.955 | 1.00 |
| 84_Y | 93_A | 1.862 | 1.00 |
| 23_D | 28_D | 1.788 | 1.00 |
| 34_S | 37_E | 1.665 | 1.00 |
| 32_V | 38_L | 1.615 | 1.00 |
| 15_W | 65_I | 1.586 | 1.00 |
| 13_K | 101_W | 1.580 | 1.00 |
| 7_Y | 25_Q | 1.577 | 1.00 |
| 19_Q | 23_D | 1.572 | 1.00 |
| 62_W | 83_A | 1.527 | 1.00 |
| 93_A | 99_R | 1.509 | 1.00 |
| 18_S | 101_W | 1.482 | 1.00 |
| 80_G | 91_S | 1.462 | 1.00 |
| 37_E | 104_S | 1.416 | 1.00 |
| 32_V | 41_L | 1.372 | 0.99 |
| 54_L | 70_W | 1.342 | 0.99 |
| 30_A | 52_I | 1.335 | 0.99 |
| 21_F | 24_S | 1.334 | 0.99 |
| 9_S | 101_W | 1.320 | 0.99 |
| 6_F | 30_A | 1.306 | 0.99 |
| 15_W | 55_S | 1.268 | 0.99 |
| 33_E | 37_E | 1.191 | 0.98 |
| 19_Q | 65_I | 1.162 | 0.97 |
| 56_R | 62_W | 1.155 | 0.97 |
| 31_Q | 66_N | 1.152 | 0.97 |
| 16_T | 57_E | 1.147 | 0.97 |
| 8_F | 50_H | 1.104 | 0.96 |
| 50_H | 100_K | 1.092 | 0.96 |
| 39_N | 42_L | 1.090 | 0.96 |
| 49_D | 84_Y | 1.079 | 0.95 |
| 56_R | 59_G | 1.079 | 0.95 |
| 4_K | 37_E | 1.071 | 0.95 |
| 31_Q | 65_I | 1.060 | 0.95 |
| 38_L | 42_L | 1.059 | 0.95 |
| 56_R | 60_Q | 1.042 | 0.94 |
| 15_W | 51_W | 1.027 | 0.94 |
| 31_Q | 104_S | 1.025 | 0.93 |
| 56_R | 81_E | 1.017 | 0.93 |
| 17_S | 20_R | 1.006 | 0.93 |
| 49_D | 93_A | 1.004 | 0.93 |
| 93_A | 97_T | 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 | |
| 4iopA | 1 | 1 | 99.8 | 0.008 | Contact Map |
| 1fm5A | 1 | 1 | 99.8 | 0.026 | Contact Map |
| 4qkhA | 2 | 1 | 99.8 | 0.027 | Contact Map |
| 3rs1A | 2 | 1 | 99.8 | 0.041 | Contact Map |
| 3c8jA | 4 | 1 | 99.8 | 0.042 | Contact Map |
| 3g8lA | 4 | 1 | 99.8 | 0.043 | Contact Map |
| 3hupA | 2 | 1 | 99.8 | 0.053 | Contact Map |
| 3g8kA | 2 | 1 | 99.8 | 0.057 | Contact Map |
| 3kqgA | 6 | 1 | 99.8 | 0.061 | Contact Map |
| 1wk1A | 1 | 1 | 99.7 | 0.065 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)