| cterm |
| ID: | 1512674826 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 106 (106) | ||
| Sequences: | 111 (51.4) | ||
| Seq/Len: | 1.047 | ||
| Nf(neff/√len): | 5.0 |
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: 1.047).
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 |
| 12_T | 29_L | 2.534 | 0.99 |
| 30_A | 36_L | 2.295 | 0.99 |
| 10_Y | 36_L | 1.900 | 0.94 |
| 103_K | 106_W | 1.851 | 0.93 |
| 51_E | 55_P | 1.818 | 0.92 |
| 19_K | 42_N | 1.748 | 0.90 |
| 102_G | 106_W | 1.615 | 0.84 |
| 25_V | 35_V | 1.615 | 0.84 |
| 56_Y | 79_N | 1.591 | 0.83 |
| 26_I | 38_F | 1.563 | 0.82 |
| 38_F | 42_N | 1.541 | 0.80 |
| 32_K | 40_N | 1.473 | 0.76 |
| 25_V | 29_L | 1.462 | 0.75 |
| 51_E | 54_A | 1.427 | 0.73 |
| 10_Y | 30_A | 1.425 | 0.73 |
| 2_G | 7_N | 1.377 | 0.69 |
| 2_G | 6_A | 1.337 | 0.66 |
| 3_Q | 7_N | 1.294 | 0.62 |
| 26_I | 30_A | 1.289 | 0.62 |
| 101_T | 106_W | 1.266 | 0.59 |
| 30_A | 38_F | 1.253 | 0.58 |
| 5_T | 36_L | 1.250 | 0.58 |
| 101_T | 104_T | 1.240 | 0.57 |
| 56_Y | 98_D | 1.238 | 0.57 |
| 51_E | 77_S | 1.233 | 0.56 |
| 92_S | 99_S | 1.226 | 0.56 |
| 90_P | 96_E | 1.216 | 0.55 |
| 101_T | 105_M | 1.200 | 0.53 |
| 14_L | 48_I | 1.190 | 0.52 |
| 9_A | 19_K | 1.185 | 0.52 |
| 5_T | 18_S | 1.182 | 0.52 |
| 61_S | 81_V | 1.174 | 0.51 |
| 9_A | 12_T | 1.162 | 0.50 |
| 5_T | 10_Y | 1.152 | 0.49 |
| 19_K | 46_D | 1.150 | 0.49 |
| 58_S | 62_S | 1.136 | 0.47 |
| 4_Q | 7_N | 1.133 | 0.47 |
| 89_R | 96_E | 1.125 | 0.46 |
| 14_L | 26_I | 1.121 | 0.46 |
| 56_Y | 88_H | 1.114 | 0.45 |
| 72_L | 88_H | 1.114 | 0.45 |
| 9_A | 29_L | 1.093 | 0.43 |
| 42_N | 46_D | 1.089 | 0.43 |
| 53_P | 56_Y | 1.075 | 0.42 |
| 28_E | 37_Q | 1.069 | 0.41 |
| 30_A | 33_D | 1.067 | 0.41 |
| 18_S | 21_E | 1.062 | 0.41 |
| 58_S | 79_N | 1.054 | 0.40 |
| 35_V | 42_N | 1.035 | 0.38 |
| 3_Q | 6_A | 1.030 | 0.38 |
| 33_D | 45_L | 1.022 | 0.37 |
| 56_Y | 80_V | 1.008 | 0.36 |
| 9_A | 45_L | 1.003 | 0.35 |
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 | |
| 4qhsA | 7 | 0.3679 | 89.1 | 0.901 | Contact Map |
| 1l8qA | 1 | 0.4811 | 89 | 0.902 | Contact Map |
| 2qbyA | 1 | 0.5283 | 88.2 | 0.903 | Contact Map |
| 4w5wA | 1 | 0.4057 | 87.6 | 0.904 | Contact Map |
| 1ofhA | 3 | 0.5566 | 85.8 | 0.906 | Contact Map |
| 3pfiA | 2 | 0.434 | 85.6 | 0.907 | Contact Map |
| 1um8A | 1 | 0.5849 | 85.6 | 0.907 | Contact Map |
| 3b9pA | 1 | 0.5849 | 85.5 | 0.907 | Contact Map |
| 1in4A | 1 | 0.4245 | 85.3 | 0.907 | Contact Map |
| 1sxjD | 1 | 0.4623 | 85.2 | 0.907 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)