Rv3050c (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: transcriptional regulator asnC-family
- REFSEQ: AsnC family transcriptional regulator
- PATRIC: Transcriptional regulator TetR family
- TUBERCULIST: Probable transcriptional regulatory protein (probably AsnC-family)
- NCBI: Probable transcriptional regulatory protein (probably AsnC-family)
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 3411217
End: 3411957
Operon:

Trans-membrane region:
Role: I.J.1 - Repressors/activators
GO terms:
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0003700 - DNA binding transcription factor activity (Uniprot)
- GO:0003677 - DNA binding (Uniprot)
- GO:0000976 - transcription regulatory region sequence-specific DNA binding (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile (Transcriptional Responses to Drugs; Boshoff et al, 2004)
Gene Modules extracted from cluster analysis of 249 transcriptomic datasets using ICA
Orthologs among selected mycobacteria
Protein structure:
Search for Homologs in PDB
Top 10 Homologs in PDB (as of Nov 2020): (none with >35% aa id)
Links to additional information on Rv3050c:
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.348 (from Jeremy Rock's lab)

Amino Acid Sequence

VVRIPRPHPSAKPGVKVDARSERWREHRKKVRNEIVDAAFRAIDRLGPELSVRQIAEEAGTAKPKIYRHFTDKSDLLEAIGMRLRDMLWAAIFPSLDLAT
DSAREVIRRSVEEYVNLVDQHPNVLRVFIQGRSAKQSEATVRTLNEGREITLAMAEMFNNELREMELNRAALELAAFAAFGSAASATEWWLGPEPDSPRR
MPREQFVAHLTTIMMGVIVGTAEALGIAVDPDQPIHDAVPNNPAVR

(Nucleotide sequence available on KEGG)

Additional Information

ESSENTIALITY

MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb

TnSeqCorr - genes with correlated TnSeq profiles across >100 conditions *new*

Classification	Condition	Strain	Method	Reference	Notes
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 8 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 8 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 8 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 8 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.929650; 7 non-insertions in a row out of 8 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.56
Non-Essential	7H09/7H10 + rich media	H37RvMA	MotifHMM	DeJesus et al. (2017)	Fully saturated (14 reps).

TnSeq Data No data currently available.

No TnSeq data currently available for this Target.

RNASeq Data No data currently available.

No RNA-Seq data currently available for this Target.

Metabolomic Profiles No data currently available.

No Metabolomic data currently available for this Target.

Proteomic Data No data currently available.

No Proteomic data currently available for this Target.

Regulatory Relationships from Systems Biology

BioCyc

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

NOTE: Green edges represent the connected genes being classified as differentially essential as a result of the middle gene being knocked out. These interactions are inferred based on RNASeq.

Interactions based on ChIPSeq data

RNA processing and modification

Energy production and conversion

Chromatin structure and dynamics

Amino acid transport and metabolism

Cell cycle control, cell division, chromosome partitioning

Carbohydrate transport and metabolism

Nucleotide transport and metabolism

Lipid transport and metabolism

Coenzyme transport and metabolism

Transcription

Translation, ribosomal structure and biogenesis

Cell wall/membrane/envelope biogenesis

Replication, recombination and repair

Posttranslational modification, protein turnover, chaperones

Cell motility

Secondary metabolites biosynthesis, transport and catabolism

Inorganic ion transport and metabolism

Function unknown

General function prediction only

Intracellular trafficking, secretion, and vesicular transport

Signal transduction mechanisms

Extracellular structures

Defense mechanisms

Nuclear structure

Cytoskeleton

BioCyc Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)

Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05).

BioCyc Transcription factor binding based on ChIP-Seq (Systems Biology)

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- Rv0113 (gmhA) (Direct binding)
- Rv0885 (-) (Direct binding)
- Rv1116 (-) (Direct binding)
- Rv2145c (wag31) (Direct binding)
- Rv3049c (-) (Direct binding)
- Rv3616c (espA) (Direct binding)
- Rv3888c (-) (Direct binding)
- Rv0114 (gmhB) (Upstream of operon)
- Rv0115 (hddA) (Upstream of operon)
- Rv0886 (fprB) (Upstream of operon)
- Rv3885c (eccE2) (Upstream of operon)
- Rv3886c (mycP2) (Upstream of operon)
- Rv3887c (eccD2) (Upstream of operon)
Bound By:
- No bindings to other targets were found.

Interactions based on TFOE data (Rustad et al. 2014)

Upregulates:
- Rv1130 (prpD)
- Rv1131 (prpC)
Upregulated by:
- Not upregulated by other genes.
Downregulates:
Downregulated by:
- Rv0452 (-)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	RegulatedBy Rv1221	yamir.moreno	IEP		Microarrays. mRNA levels of regulated element measured and compared between wild-type and trans-element mutation (knockout, over expression etc.) performed by using microarray (or macroarray) experiments.. PA. Fontn, V. Aris et al. Mycobacterium tuberculosis Sigma Factor E Regulon Modulates the Host Inflammatory Response. J. Infect. Dis. 2008
Interaction	RegulatedBy Rv3676	yamir.moreno	TAS		Literature previously reported link (from Balazsi et al. 2008). Traceable author statement to experimental support. G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008

TB Genome Annotation Portal