Rv1985c HTH-type transcriptional regulator

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1985c HTH-type transcriptional regulator CDS 2228991 2229902 - 912 303 TRUE

Rv1985c (HTH-type transcriptional regulator) is predicted to be co-regulated in modules bicluster_0007 with residual 0.55 and bicluster_0380 with residual 0.52.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 0.00 and 0.00 for bicluster_0007 and 0.07 and 0.10 for bicluster_0380 respectively.

These modules are enriched for following go terms: .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 147
Gene Target Differential Expression Distance Expression pvalue Type
Transcriptional regulator, GntR family
No -2 -0.25 0.380591 CDS
PROBABLE MEMBRANE PROTEIN
No 62 -0.17 0.628344 Antisense.TSS
Formate hydrogenlyase subunit 11
No 30 -0.46 0.390195 Primary.TSS
Phosphoheptose isomerase (EC 5.3.1.-)
No -72 0.12 0.762759 CDS
No -77 0.29 0.372037 Primary.TSS
tRNA (guanine46-N7-)-methyltransferase (EC 2.1.1.33)
No -6 0.26 0.18753 Internal.TSS
PROBABLE CONSERVED TRANSMEMBRANE PROTEIN
No 9 -0.27 0.416869 CDS
No -18 -0.07 0.87439 Primary.TSS
Possible conserved exported protein
No -36 -0.29 0.579344 CDS
No 52 -0.2 0.57443 CDS
Displaying 1 - 10 of 10
ChipSeq TF Differential Expression Distance Expression pvalue Type
Two component DNA binding Transcriptional regulatory protein TcrA
No 68 -0.49 0.274709 CDS
transcriptional regulator, ArsR family
Induced 34 0.92 0.000000221 Internal.TSS
Organic hydroperoxide resistance transcriptional regulator
Repressed 52 -0.7 0.0458282 CDS
Transcriptional regulator, TetR family
No 31 0.13 0.839969 Internal.TSS
transcriptional regulator, ArsR family
Induced 61 0.92 0.000000221 CDS
putative two-component system response regulator
No 62 -0.3 0.48492 CDS
Transcriptional regulator, ArsR family
Repressed 67 -1.12 0.000000000319 CDS
HTH-type transcriptional regulator
Induced 65 5.07 0 CDS
TetR/ACRR family transcriptional regulator
No 61 -0.03 0.992748 Internal.TSS
No 67 0.19 0.5965 CDS
Motif 1 Motif 2 Residual
bicluster_0007
e.value: 
0.0000000091
Motif Bicluster: 
e.value: 
0.00042
Motif Bicluster: 
0.55
bicluster_0380
e.value: 
0.066
Motif Bicluster: 
e.value: 
0.096
Motif Bicluster: 
0.52
Product (LegacyBRC) Product (RefSeq)
Uncharacterized HTH-type transcriptional regulator Rv1985c_MT2039 chromosome replication initiation inhibitor protein
Operon # Operon
1297
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
15609122 NP_216501.1 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 GSM1426758 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426759 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426761 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426762 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426758 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426759 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426761 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426762 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426758 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426759 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1985c_B124 UCSC Browser Tracks
Rv1985c_B215 UCSC Browser Tracks
Rv1985c_B559 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
0.110000 0.83

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: 0.00135884
p-value INH: 0.952622
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 8.34 U
D3I 3 3 3.83 7.89 I
D3U 3 3 3.83 8.32 U
D5I 9 5 6.00 10.84 I
D5U 17 5 6.00 11.33 U
D7I 18 7 8.14 6.54 I
D7U 19 7 8.14 7.53 U
D14I 4 14 15.63 3.27 I
D14U 4 14 15.63 6.73 U
D17I 3 17 19.15 I
D17U 3 17 19.15 5.97 U
D21I 4 21 23.23 2.50 I
D21U 4 21 23.23 6.26 U
D24I 3 24 26.60 I
D24U 3 24 26.60 5.95 U
D28I 4 28 30.61 I
D28U 4 28 30.61 5.77 U