| Q |
| ID: | 1496148158 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 109 (107) | ||
| Sequences: | 311 (282.9) | ||
| Seq/Len: | 2.907 | ||
| Nf(neff/√len): | 27.3 |
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: 2.907).
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 |
| 3_A | 41_A | 3.552 | 1.00 |
| 46_V | 94_L | 2.580 | 1.00 |
| 16_L | 36_V | 1.986 | 1.00 |
| 33_P | 102_E | 1.895 | 0.99 |
| 44_G | 93_G | 1.875 | 0.99 |
| 17_L | 96_F | 1.685 | 0.98 |
| 42_T | 93_G | 1.683 | 0.98 |
| 14_D | 35_F | 1.625 | 0.97 |
| 32_K | 96_F | 1.624 | 0.97 |
| 39_G | 99_R | 1.464 | 0.95 |
| 11_S | 21_N | 1.439 | 0.94 |
| 11_S | 60_V | 1.418 | 0.93 |
| 45_R | 99_R | 1.415 | 0.93 |
| 62_G | 77_E | 1.402 | 0.93 |
| 16_L | 37_V | 1.394 | 0.92 |
| 12_Y | 16_L | 1.354 | 0.91 |
| 2_K | 44_G | 1.307 | 0.89 |
| 94_L | 99_R | 1.301 | 0.89 |
| 40_V | 95_D | 1.290 | 0.88 |
| 48_M | 88_V | 1.285 | 0.88 |
| 50_E | 84_S | 1.268 | 0.87 |
| 34_M | 46_V | 1.259 | 0.86 |
| 37_V | 70_G | 1.255 | 0.86 |
| 55_T | 75_G | 1.246 | 0.86 |
| 42_T | 49_K | 1.199 | 0.82 |
| 37_V | 81_S | 1.183 | 0.81 |
| 13_M | 103_F | 1.164 | 0.80 |
| 20_K | 23_I | 1.157 | 0.79 |
| 68_V | 97_A | 1.153 | 0.79 |
| 36_V | 101_R | 1.141 | 0.78 |
| 73_E | 77_E | 1.130 | 0.77 |
| 38_V | 41_A | 1.116 | 0.76 |
| 82_D | 88_V | 1.114 | 0.75 |
| 8_A | 15_V | 1.114 | 0.75 |
| 52_R | 95_D | 1.101 | 0.74 |
| 81_S | 97_A | 1.097 | 0.74 |
| 9_D | 99_R | 1.090 | 0.73 |
| 8_A | 94_L | 1.059 | 0.70 |
| 17_L | 105_Y | 1.054 | 0.70 |
| 42_T | 90_G | 1.051 | 0.69 |
| 43_A | 95_D | 1.050 | 0.69 |
| 20_K | 35_F | 1.049 | 0.69 |
| 14_D | 25_Y | 1.046 | 0.69 |
| 5_V | 97_A | 1.043 | 0.68 |
| 2_K | 78_R | 1.033 | 0.67 |
| 2_K | 6_F | 1.027 | 0.67 |
| 57_K | 85_C | 1.015 | 0.65 |
| 11_S | 76_L | 1.013 | 0.65 |
| 60_V | 79_E | 1.009 | 0.65 |
| 5_V | 88_V | 1.005 | 0.64 |
| 25_Y | 102_E | 1.000 | 0.64 |
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 | |
| 4jx2A | 2 | 0.8899 | 10.5 | 0.916 | Contact Map |
| 2hyeC | 1 | 0.3394 | 4.9 | 0.927 | Contact Map |
| 3mmyB | 4 | 0.2569 | 4.9 | 0.928 | Contact Map |
| 2joyA | 1 | 0.3394 | 4.8 | 0.928 | Contact Map |
| 2lo0A | 2 | 0.3486 | 4.7 | 0.928 | Contact Map |
| 3dplC | 1 | 0.3394 | 4.6 | 0.929 | Contact Map |
| 4kwbA | 8 | 0.1101 | 4.4 | 0.929 | Contact Map |
| 2v0cA | 1 | 0 | 3.9 | 0.931 | Contact Map |
| 4arcA | 1 | 0.422 | 3.7 | 0.932 | Contact Map |
| 2cmpA | 1 | 0.2844 | 2.9 | 0.935 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)