O1 operator-only Sort-Seq libraries were assayed at R≈130 with three LacI DNA-binding-domain variants (Y20I, Q21A, and Q21M). The table summarizes the inferred relative substitution effects for each protein background.
Processed tables are specific to each experiment. Column names, units, measurements, and table structure are not standardized across the database. Check this experiment’s column definitions and quality-control notes before comparing or combining data.
Organism
NCBITaxon:511145
Taxonomy ID
NCBITaxon:511145
Biosample
UNMAPPED:Escherichia_coli_K-12_MG1655_culture
Reference genome
Not reported / not applicable
Design focus
Synthetic / Motif-focused
Region of interest
Not reported / not applicable
Perturbation & assay details
LacI DNA-binding-domain variants Y20I, Q21A, and Q21M; basal reporter condition; approximately R=130 tetramers
episomal pUA66 operator-GFP reporter; each protein mutant has three split energy matrices in arbitrary units (au), so values are comparable within but not across protein backgrounds without additional scaling.
Processed data
50 rows per page. Click a cell to inspect its full value.
Visible columns (29 of 29)
Row
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
Page 1 · 50 rows · More results available
Filters apply to this table only. The CSV download contains the complete processed table; filtered rows are available through the API.
Column dictionary · 29 definitions
record_type
Whether the row is an MPRA matrix-derived single-base substitution or a published flow-cytometry validation record.
model_id
Source S1 Models filename or compact repository summary filename.
library_design
Reporter-library design used for the matrix.
regulatory_context
Position of the LacI operator relative to the RNAP binding site.
reference_operator
Wild-type operator sequence used to design the library.
matrix_operator
Operator whose Sort-Seq matrix was used for the prediction.
reference_sequence
Reference DNA sequence for the matrix/library.
variant_id
Stable descriptive identifier for the substitution or validation mutant.
variant_sequence
21-bp operator sequence carrying the indicated substitution(s).
mutation_count
Number of sequence differences from the relevant reference sequence.
position_1based
1-based operator position for single-base substitutions; blank for multi-base validation records.
reference_base
Reference nucleotide at position_1based.
alternate_base
Alternative nucleotide at position_1based.
lacI_variant
LacI protein background used for the model.
lacI_copy_number_tetramers
Approximate mean LacI tetramer copy number R in the strain.
biological_day
Biological collection day when separately reported by the source model.
replicate_count
Number of split or biological replicate matrices summarized in the mean/SD.
matrix_energy_unit
Energy unit reported by the source matrix: kBT or arbitrary units (au).
delta_binding_energy_mean
Mean predicted binding-energy change for the alternative base relative to the matrix reference base; negative means stronger binding.
delta_binding_energy_sd
Standard deviation of the predicted relative binding-energy change across source matrix replicates.
Maximum replicate predicted relative binding-energy change.
predicted_binding_energy_kBT
Absolute predicted LacI binding energy in kBT when the source provides a kBT-scaled R=130 matrix.
predicted_binding_energy_sd_kBT
SD of the absolute kBT prediction across matrix replicates.
published_prediction_mean_kBT
Published mean binding-energy prediction from the repository validation summary.
published_prediction_sd_kBT
Published SD of the validation prediction.
published_measured_binding_energy_kBT
Published binding energy measured by fitting conventional flow-cytometry fold-change curves.
effect_direction
Interpretation of delta binding energy: stronger, weaker, or no_change relative to the reference.
qc_pass
True when all required sequence/matrix values are finite and the row passed package QC.
Quality control
The paper’s stated sequencing QC was applied before matrix inference: per-base PHRED score >20, with approximately 300,000–500,000 useful reads per bin after filtering. The paper used four FACS bins (each approximately 15% of the fluorescence histogram), at least 10^6 transformants per library, and Bayesian energy-matrix inference with three non-overlapping split replicates. Package QC retained only rows with a 21-bp sequence, valid A/C/G/T matrix entries, finite replicate aggregates, and qc_pass=true. Published validation records are retained only when their reported prediction/measurement values are finite.
Curation notes
The published S1 Models archive is the source for matrix rows. Matrix values are converted to alternative-base minus reference-base values at each position. Negative values indicate a more favorable/more negative predicted LacI binding energy. The first experiment includes published flow-cytometry validation records as record_type=published_flow_cytometry_validation; these are not raw Sort-Seq sequence counts and are kept distinct from MPRA matrix rows. R=130 full-promoter matrices are the primary kBT-scaled results; other model contexts are reported in au as supplied by the authors.