Rv1990c

Summary
Product Feature Type Start End Strand Length AA Length is TF
Rv1990c CDS 2233296 2233637 - 342 113 TRUE

Rv1990c () is predicted to be co-regulated in modules bicluster_0220 with residual 0.49 and bicluster_0397 with residual 0.58.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 9.80 and 4,900.00 for bicluster_0220 and 0.00 and 0.00 for bicluster_0397 respectively.

These modules are enriched for following go terms: nitrogen compound metabolic process, carbon-oxygen lyase activity.

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 10 of 122
Gene Target Differential Expression Distance Expression pvalue Type
transcriptional regulator, ArsR family
No -101 -0.39 0.770839 Primary.TSS
D,D-heptose 7-phosphate kinase
Repressed -124 -0.72 0.0478728 Antisense.TSS
Histone acetyltransferase HPA2 and related acetyltransferases
No 34 0.1 0.820966 Primary.TSS
No 44 -0.19 0.681334 CDS
Butyryl-CoA dehydrogenase (EC 1.3.99.2)
No 19 -0.05 0.937133 Primary.TSS
POSSIBLE EXPORTED PROTEIN
No 5 0.16 0.837771 CDS
tRNA (guanine46-N7-)-methyltransferase (EC 2.1.1.33)
Repressed 6 -0.88 0.0000000305 Internal.TSS
No -126 -0.36 0.221585 Primary.TSS
Aldehyde dehydrogenase (EC 1.2.1.3)
No 38 -0.19 0.735011 Antisense.TSS
Glycosyltransferase (EC 2.4.1.-)
No 9 -0.43 0.00390024 Primary.TSS
Displaying 1 - 3 of 3
ChipSeq TF Differential Expression Distance Expression pvalue Type
Histone protein Lsr2
No 24 0.17 0.816642 CDS
Beta-carotene ketolase (EC 1.14.-.-)
No 28 0.09 0.999473 CDS
Transcriptional regulator, MarR family
No 25 -0.26 0.579028 CDS
Motif 1 Motif 2 Residual
bicluster_0220
e.value: 
9.8
Motif Bicluster: 
e.value: 
4900
Motif Bicluster: 
0.49
bicluster_0397
e.value: 
0.000000000016
Motif Bicluster: 
e.value: 
0.000063
Motif Bicluster: 
0.58
Product (LegacyBRC) Product (RefSeq)
Uncharacterized protein Rv1990c_MT2044 transcriptional regulatory protein
Operon # Operon
1303 -
PATRIC Locus Tag Enzyme Name PATRIC Pathways Transcriptomics
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
15609127 NP_216506.1 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 GSM1426763 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426764 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1426765 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv1990c_B324 UCSC Browser Tracks
Quantitative Proteomics Data
t-test p-value Cholesterol/Glycerol Ratio
NA NA

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:
p-value INH: