Rv3676 cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases

Summary
Symbol Product Feature Type Start End Strand Length AA Length is TF
Rv3676 crp cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein... CDS 4116478 4117152 + 675 224 TRUE

Rv3676 (cAMP-binding proteins - catabolite gene activator and regulatory subunit of cAMP-dependent protein kinases) is predicted to be co-regulated in modules bicluster_0349 with residual 0.51 and bicluster_0472 with residual 0.59.

This regulation is possibly mediated by two de-novo identified cis-regulatory motifs in each module with e-values , 2.40 and 4,600.00 for bicluster_0349 and 0.01 and 1.70 for bicluster_0472 respectively.

These modules are enriched for following go terms: lipopolysaccharide metabolic process, lipopolysaccharide biosynthetic process, carbon-carbon lyase activity, oxo-acid-lyase activity .

This gene is found to be for growth on cholesterol.

Mutant available?:

Displaying 1 - 9 of 9
Gene Target Differential Expression Distance Expression pvalue Type
Possible membrane protein
No -71 -0.06 0.946187 CDS
No -2 -0.05 0.966904 CDS
membrane protein, MmpS family
No -6 -0.32 0.583208 Primary.TSS
Transcriptional regulator, TetR family
No -52 0.36 0.780321 CDS
Transcriptional regulator, TetR family
No -70 0.36 0.780321 Internal.TSS
Succinyl-CoA ligase [ADP-forming] beta chain (EC 6.2.1.5)
No -85 0.18 0.711689 Primary.TSS
PE family protein
Induced -26 1.66 0.0108887 Primary.TSS
POSSIBLE SECRETED ALANINE RICH PROTEIN
No -131 -0.05 0.964305 Primary.TSS
WhiB-type transcription regulator
No -63 0.37 0.0771035 Primary.TSS
Displaying 1 - 2 of 2
ChipSeq TF Differential Expression Distance Expression pvalue Type
transcriptional regulator, ArsR family
No -23 0.29 0.015869 Primary.TSS
DNA-binding response regulator mtrA
No -45 0.19 0.704151 Primary.TSS
Motif 1 Motif 2 Residual
bicluster_0349
e.value: 
2.4
Motif Bicluster: 
e.value: 
4600
Motif Bicluster: 
0.51
bicluster_0472
e.value: 
0.0071
Motif Bicluster: 
e.value: 
1.7
Motif Bicluster: 
0.59
Product (LegacyBRC) Product (RefSeq)
PROBABLE TRANSCRIPTIONAL REGULATORY PROTEIN [PROBABLY CRP_FNR-FAMILY] CRP/FNR family transcriptional regulator
Operon # Operon
2392
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
15610812 NP_218193.1 Run
GO:0003677

DNA binding

DNA binding

Details: 
Any molecular function by which a gene product interacts selectively with DNA (deoxyribonucleic acid).
GO Category: 
molecular_function
37
Total items in this category:  
GO:0005886

plasma membrane

plasma membrane

Details: 
The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
GO Category: 
cellular_component
1284
Total items in this category:  
GO:0045892

negative regulation of transcription, DNA-dependent

negative regulation of transcription, DNA-dependent

Details: 
Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
10
Total items in this category:  
GO:0030552

cAMP binding

cAMP binding

Details: 
Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
GO Category: 
molecular_function
1
Total items in this category:  
GO:0040007

growth

growth

Details: 
The increase in size or mass of an entire organism, a part of an organism or a cell.
GO Category: 
biological_process
621
Total items in this category:  
GO:0042803

protein homodimerization activity

protein homodimerization activity

Details: 
Interacting selectively and non-covalently with an identical protein to form a homodimer.
GO Category: 
molecular_function
83
Total items in this category:  
GO:0045893

positive regulation of transcription, DNA-dependent

positive regulation of transcription, DNA-dependent

Details: 
Any process that activates or increases the frequency, rate or extent of cellular DNA-dependent transcription.
GO Category: 
biological_process
14
Total items in this category:  
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 GSM1427020 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427021 GSE59086 25232098 GEO Tiling Array RNA
PRJNA254351 GSM1427022 GSE59086 25232098 GEO Tiling Array RNA
Experiment UCSC Genome Browser
Rv3676_B640 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: 0.0000000067561
p-value INH: 0.0215916
Displaying 1 - 17 of 17
Condition Count Day Doublings Fitness U.I Plots
D0U 27 0 0.00 12.41 U
D3I 3 3 3.83 12.17 I
D3U 3 3 3.83 12.20 U
D5I 9 5 6.00 11.87 I
D5U 17 5 6.00 14.77 U
D7I 18 7 8.14 8.26 I
D7U 19 7 8.14 11.85 U
D14I 4 14 15.63 2.58 I
D14U 4 14 15.63 10.65 U
D17I 3 17 19.15 2.31 I
D17U 3 17 19.15 10.48 U
D21I 4 21 23.23 2.50 I
D21U 4 21 23.23 9.50 U
D24I 3 24 26.60 2.33 I
D24U 3 24 26.60 10.29 U
D28I 4 28 30.61 1.73 I
D28U 4 28 30.61 9.47 U