| 1PSF |
| ID: | 1429466907 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 75% gaps before running GREMLIN. |
| Length: | 70 (70) | ||
| Sequences: | 120 (52) | ||
| Seq/Len: | 1.714 | ||
| Nf(neff/√len): | 6.2 |
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: 1.714).
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 |
| 7_S | 68_V | 2.322 | 1.00 |
| 63_E | 66_L | 2.293 | 1.00 |
| 30_K | 63_E | 2.168 | 0.99 |
| 19_Y | 61_F | 1.945 | 0.98 |
| 5_R | 29_D | 1.944 | 0.98 |
| 21_D | 43_K | 1.741 | 0.96 |
| 24_T | 57_N | 1.550 | 0.91 |
| 7_S | 20_G | 1.413 | 0.84 |
| 32_G | 58_T | 1.389 | 0.83 |
| 14_K | 19_Y | 1.379 | 0.82 |
| 38_I | 42_N | 1.366 | 0.81 |
| 48_G | 52_S | 1.343 | 0.80 |
| 14_K | 30_K | 1.268 | 0.74 |
| 14_K | 21_D | 1.263 | 0.74 |
| 24_T | 54_G | 1.259 | 0.74 |
| 8_K | 22_V | 1.253 | 0.73 |
| 15_E | 35_Y | 1.238 | 0.72 |
| 27_S | 55_G | 1.227 | 0.71 |
| 47_N | 53_A | 1.224 | 0.71 |
| 12_L | 20_G | 1.204 | 0.69 |
| 4_E | 42_N | 1.180 | 0.66 |
| 36_P | 52_S | 1.162 | 0.65 |
| 44_V | 57_N | 1.138 | 0.62 |
| 20_G | 55_G | 1.132 | 0.62 |
| 29_D | 33_I | 1.127 | 0.61 |
| 20_G | 62_A | 1.125 | 0.61 |
| 8_K | 24_T | 1.120 | 0.60 |
| 6_G | 62_A | 1.102 | 0.59 |
| 40_R | 45_N | 1.080 | 0.56 |
| 50_S | 53_A | 1.079 | 0.56 |
| 40_R | 60_N | 1.077 | 0.56 |
| 25_V | 59_N | 1.076 | 0.56 |
| 40_R | 46_Y | 1.067 | 0.55 |
| 48_G | 53_A | 1.062 | 0.54 |
| 2_A | 67_E | 1.060 | 0.54 |
| 19_Y | 47_N | 1.052 | 0.53 |
| 49_F | 52_S | 1.052 | 0.53 |
| 5_R | 26_A | 1.051 | 0.53 |
| 29_D | 37_V | 1.027 | 0.51 |
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 | |
| 4kt0E | 1 | 0.9714 | 100 | 0.006 | Contact Map |
| 1jb0E | 1 | 0.9714 | 100 | 0.056 | Contact Map |
| 2wscE | 1 | 0.9 | 100 | 0.151 | Contact Map |
| 1qp2A | 1 | 0.8857 | 100 | 0.26 | Contact Map |
| 2jz2A | 1 | 0.8 | 69.2 | 0.891 | Contact Map |
| 4l0jA | 1 | 0.8286 | 65.6 | 0.893 | Contact Map |
| 1dj7B | 1 | 0.7857 | 47 | 0.904 | Contact Map |
| 4tkoB | 1 | 0.8 | 24.5 | 0.918 | Contact Map |
| 2qqrA | 2 | 0.7714 | 18.4 | 0.923 | Contact Map |
| 3h8zA | 1 | 0.8286 | 17.5 | 0.923 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)