Rv2779c Transcriptional regulator, AsnC family

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv2779c Transcriptional regulator, AsnC family CDS 3086215 3086754 - 540 179 TRUE

Rv2779c (Transcriptional regulator, AsnC family) is predicted to be co-regulated in modules bicluster_0487 with residual 0.48 and bicluster_0552 with residual 0.57.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 3.50 for bicluster_0487 and 0.00 and 0.00 for bicluster_0552 respectively.

These modules are enriched for following go terms: IMP biosynthetic process, 'de novo' IMP biosynthetic process, IMP metabolic process.

This gene is found to be for growth on cholesterol.

Mutant available?:

BASS Score Distance to Tuberculist Start Codon Internal TSS New Internal UTR Re-Annotated Start Tuberculist Annotated Start
-0.29 42 3086712 102 3086610 3086754
Displaying 1 - 3 of 3
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, AsnC family
Induced -4 3.74 5.39e-36 Internal.TSS
Transcriptional regulator, AsnC family
Induced -46 3.74 5.39e-36 CDS
Alanine dehydrogenase (EC 1.4.1.1)
No -91 0.5 0.487278 Primary.TSS
Displaying 1 - 10 of 34
ChipSeq TF Differential Expression Distance Expression pvalue Type
Histone protein Lsr2
No 2 0.1 0.890683 CDS
Transcriptional repressor EthR, TetR family
No 45 0.02 0.990244 Internal.TSS
HTH-type transcriptional regulator
No 59 -0.26 0.538269 Internal.TSS
Possible oxidoreductase subunit
No -17 0.24 0.634596 CDS
Transcriptional regulator, IclR family
No -4 0.13 0.895345 CDS
WhiB-type transcription regulator
No 46 0.58 0.999973 Internal.TSS
DNA-binding response regulator
Induced -7 1.87 0.000000000000161 CDS
Transcriptional regulatory protein
Repressed 6 -1.82 0.000000000103 CDS
putative two-component system response regulator
No 1 -0.71 0.0770693 CDS
Mycofactocin system transcriptional regulator
No -129 0.23 0.999588 CDS
Product (LegacyBRC) Product (RefSeq)
POSSIBLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY LRP_ASNC-FAMILY] LRP/AsnC family transcriptional regulator
Operon # Operon
1827 -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics

PATRIC

Not assigned Not assigned
Locus Tuberculist Genome View

Tuberculist

Quickview
Locus Tag KEGG Pathways

KEGG

not assigned to any KEGG Pathway.
BioCyc Gene Page Cellular Overview Map
Link to STRING STRING Network

STRING

GI Number Protein ID Blast Conserved Domains
57117025 NP_217295.2 Run
Description:Expression data from transcription factor over expression experiments. TFOE are matched to the ChIP-seq experiment done simultaneously. This dataset is described in Rustad et al. 2014, Genome Biology.
BioProject Accession GEO Series References Repository Sample Method Sample Type
PRJNA254351 GSM1426871 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426872 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426873 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426871 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426872 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426873 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv2779c_B490 UCSC Browser Tracks
Rv2779c_B625 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.470000 1.29

How essentiality calculations were done?

The relative representation of each mutant was determined by calculating the fold change (sequence reads/insertion in cholesterol divided by sequence reads/insertion in glycerol) for each gene. Statistical significance was determined by t-test. Each insertion site in each replicate sample was treated as a separate data point. The hyperbola used for defining genes specifically required for growth in cholesterol was defined by the formula, y = 3.8/x+0.7. Genes above this line are annotated as required for growth on cholesterol.

TRIP log2 fold abundance change

reports the log2 abundance fold change of each TFI strain, relative to no induction, in absence or presence of drug, averaged across experimental replicates. Also reported are the accompanying z-scores and two-sided t-test p-values for each TFI strain under each condition. Please refer to Ma et al., 2020, Nature Microbiology for more information.

p-value Untreated: 0.0395882
p-value INH: 0.988908
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D17I 3 17 19.15 14.78 I
D17U 3 17 19.15 13.39 U
D24I 3 24 26.60 14.83 I
D24U 3 24 26.60 13.19 U
D3I 3 3 3.83 13.92 I
D3U 3 3 3.83 14.82 U
D14I 4 14 15.63 14.83 I
D14U 4 14 15.63 13.71 U
D21I 4 21 23.23 14.89 I
D21U 4 21 23.23 13.65 U
D28I 4 28 30.61 14.99 I
D28U 4 28 30.61 13.36 U
D5I 9 5 6.00 13.72 I
D5U 17 5 6.00 13.44 U
D7I 18 7 8.14 14.10 I
D7U 19 7 8.14 13.49 U
D0U 27 0 0.00 13.93 U