| SRF-Lum trimmed |
| ID: | 1424910085 |
Query Sequence |
Download Alignment We filter this alignment to remove positions that have > 50% gaps before running GREMLIN. |
| Length: | 107 (103) | ||
| Sequences: | 225 (163.5) | ||
| Seq/Len: | 2.184 | ||
| Nf(neff/√len): | 16.1 |
Jackhmmer Results: (2015_01_07)
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: 2.184).
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 |
| 49_I | 75_F | 2.715 | 1.00 |
| 49_I | 100_L | 2.046 | 0.99 |
| 23_S | 28_P | 1.907 | 0.99 |
| 17_Y | 45_T | 1.716 | 0.97 |
| 69_L | 73_Y | 1.681 | 0.96 |
| 19_R | 57_D | 1.602 | 0.95 |
| 32_L | 49_I | 1.554 | 0.94 |
| 84_G | 90_D | 1.549 | 0.94 |
| 32_L | 100_L | 1.510 | 0.93 |
| 67_T | 91_Q | 1.503 | 0.92 |
| 29_I | 99_G | 1.486 | 0.92 |
| 57_D | 62_Q | 1.479 | 0.92 |
| 7_L | 53_N | 1.475 | 0.91 |
| 53_N | 61_V | 1.464 | 0.91 |
| 98_C | 102_Y | 1.457 | 0.91 |
| 54_K | 64_E | 1.450 | 0.91 |
| 78_T | 100_L | 1.441 | 0.90 |
| 33_K | 101_E | 1.436 | 0.90 |
| 21_T | 25_R | 1.431 | 0.90 |
| 23_S | 26_L | 1.422 | 0.89 |
| 8_R | 56_W | 1.406 | 0.89 |
| 4_R | 86_E | 1.403 | 0.89 |
| 36_G | 40_G | 1.398 | 0.88 |
| 75_F | 100_L | 1.371 | 0.87 |
| 36_G | 73_Y | 1.328 | 0.85 |
| 44_Y | 67_T | 1.306 | 0.83 |
| 3_D | 95_R | 1.299 | 0.83 |
| 8_R | 12_A | 1.278 | 0.81 |
| 11_K | 61_V | 1.255 | 0.80 |
| 97_S | 102_Y | 1.248 | 0.79 |
| 25_R | 96_G | 1.186 | 0.74 |
| 100_L | 104_L | 1.184 | 0.74 |
| 44_Y | 69_L | 1.155 | 0.71 |
| 50_Q | 62_Q | 1.149 | 0.71 |
| 16_H | 77_K | 1.142 | 0.70 |
| 93_V | 105_D | 1.140 | 0.70 |
| 36_G | 44_Y | 1.126 | 0.68 |
| 38_T | 64_E | 1.124 | 0.68 |
| 87_S | 93_V | 1.108 | 0.67 |
| 17_Y | 47_K | 1.107 | 0.67 |
| 47_K | 74_K | 1.100 | 0.66 |
| 3_D | 74_K | 1.078 | 0.64 |
| 15_L | 99_G | 1.063 | 0.62 |
| 14_T | 80_V | 1.051 | 0.61 |
| 27_D | 54_K | 1.047 | 0.60 |
| 16_H | 72_A | 1.045 | 0.60 |
| 6_L | 89_E | 1.044 | 0.60 |
| 31_Q | 83_E | 1.023 | 0.58 |
| 18_D | 35_V | 1.023 | 0.58 |
| 54_K | 61_V | 1.020 | 0.57 |
| 37_G | 57_D | 1.018 | 0.57 |
| 98_C | 104_L | 1.015 | 0.57 |
| 30_P | 33_K | 1.014 | 0.57 |
| 16_H | 46_P | 1.013 | 0.56 |
| 4_R | 37_G | 1.011 | 0.56 |
| 6_L | 9_D | 1.006 | 0.56 |
| 12_A | 45_T | 1.004 | 0.55 |
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 | |
| 3rgaA | 1 | 0.3458 | 6.1 | 0.948 | Contact Map |
| 2l5qA | 1 | 0.3364 | 5.8 | 0.949 | Contact Map |
| 3bjsA | 2 | 0.2804 | 4.8 | 0.951 | Contact Map |
| 3wmdA | 2 | 0.3364 | 4.7 | 0.951 | Contact Map |
| 3b9oA | 2 | 0.3271 | 3.6 | 0.954 | Contact Map |
| 1ewsA | 1 | 0.2523 | 3.1 | 0.955 | Contact Map |
| 1ohpA | 4 | 0.3364 | 3 | 0.956 | Contact Map |
| 1fizL | 1 | 0.1215 | 3 | 0.956 | Contact Map |
| 1kqhA | 1 | 0.2243 | 2.8 | 0.956 | Contact Map |
| 1fiwL | 1 | 0.1308 | 2.7 | 0.957 | Contact Map |
Cov = coverage of hit
P(%) = probability
Sequence Conservation (Image Generated using WebLogo v3)