Rv3031 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: hypothetical protein
- PATRIC: Glycogen branching enzyme GH-57-type archaeal (EC 2.4.1.18)
- TUBERCULIST: Conserved protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: -
  - function: possible paralog of GlgB; probable 1,4-alpha-glucan branching enzyme
  - reference: Stadthagen (2007) PMID: 17640872; Grzegorzewicz (2025) PMID: 40295170
Coordinates in H37Rv: 3389922 - 3391502
Gene length: 1581 bp (with stop codon), 526 aa (without stop codon)
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0102752 - 1,4-alpha-glucan branching enzyme activity (using a glucosylated glycogenin as primer for glycogen synthesis) (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0016757 - transferase activity, transferring glycosyl groups (Uniprot)
- GO:0016740 - transferase activity (Uniprot)
- GO:0005975 - carbohydrate metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0003844 - 1,4-alpha-glucan branching enzyme activity (Uniprot)
- GO:0003824 - catalytic activity (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 Latest Homologs in PDB
Top 10 Homologs in PDB (as of Apr 2026): (none with >35% aa id)
Links to additional information on Rv3031:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -3.689 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

LNTSASPVPGLFTLVLHTHLPWLAHHGRWPVGEEWLYQSWAAAYLPLLQVLAALADENRHRLITLGMTPVVNAQLDDPYCLNGVHHWLANWQLRAEEAAS
VRYARQSKSADYPSCTPEALRAFGIRECADAARALDNFATRWRHGGSPLLRGLIDAGTVELLGGPLAHPFQPLLAPRLREFALREGLADAQLRLAHRPKG
IWAPECAYAPGMEVDYATAGVSHFMVDGPSLHGDTALGRPVGKTDVVAFGRDLQVSYRVWSPKSGYPGHAAYRDFHTYDHLTGLKPARVTGRNVPSEQKA
PYDPERADRAVDVHVADFVDVVRNRLLSESERIGRPAHVIAAFDTELFGHWWYEGPTWLQRVLRALPAAGVRVGTLSDAIADGFVGDPVELPPSSWGSGK
DWQVWSGAKVADLVQLNSEVVDTALTTIDKALAQTASLDGPLPRDHVADQILRETLLTVSSDWPFMVSKDSAADYARYRAHLHAHATREIAGALAAGRRD
TARRLAEGWNRADGLFGALDARRLPK

(Nucleotide sequence available on KEGG)

Additional Information

possible paralog of GlgB
probable 1,4-alpha-glucan branching enzyme

ESSENTIALITY

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

TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv3031/-, gene len: 1580 bp, num TA sites: 20

condition	dataset	call	medium	method	notes
in-vitro	DeJesus 2017 mBio	essential	7H9	HMM	fully saturated, 14 TnSeq libraries combined
in-vitro	Sassetti 2003 Mol Micro	essential	7H9	TRASH	essential if hybridization ratio<0.2
in-vivo (mice)	Sassetti 2003 PNAS	non-essential	BL6 mice	TRASH	essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol)	Griffin 2011 PPath	essential	M9 minimal+glycerol	Gumbel	2 replicates; Padj<0.05
in-vitro (cholesterol)	Griffin 2011 PPath	essential	M9 minimal+cholesterol	Gumbel	3 replicates; Padj<0.05
differentially essential in cholesterol	Griffin 2011 PPath	NO (LFC=0.0)	cholesterol vs glycerol	resampling-SR	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro	Smith 2022 eLife	essential	7H9	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice)	Smith 2022 eLife	essential	BL6 mice	HMM	6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice	Smith 2022 eLife	NO (LFC=0.0)	in-vivo vs in-vitro	ZINB	YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal)	Minato 2019 mSys	non-essential	minimal medium	HMM
in-vitro (YM rich medium)	Minato 2019 mSys	essential	YM rich medium	HMM	7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium	Minato 2019 mSys	YES (LFC=-3.8)	YM rich vs minimal medium	resampling

Analysis of Positive Selection in Clinical Isolates new

data from Culviner et al (2025) (55,259 Mtb clinical isolates)
- overall pN/pS for Rv3031: 0.482837928
- lineage-specific pN/pS in L1: 0.489431303
- lineage-specific pN/pS in L2: 0.418548149
- lineage-specific pN/pS in L3: 0.379680041
- lineage-specific pN/pS in L4: 0.537836597

Analysis of dN/dS (omega) in a global collection of 10k Mtb clinical isolates using GenomegaMap (Window model)
clinical isolates collection: global set of 10,626 Mtb genomes
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.

	global set of 10,626 Mtb clinical isolates
under significant positive selection?	NO
omega peak height (95%CI lower bound)	1.66 (0.51)
codons under selection
omega plots
genetic variants*	link

* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"

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: see table of TFOE interactions below

Interactions based on ChIPSeq data

Binds To:
- No bindings to other targets were found.
Bound By:

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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv1353c (-) (Direct binding)
- Rv0238 (-) (Upstream of operon)
- Rv2034 (-) (Upstream of operon)

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

TFOE = Transcription Factor Over-Expression study
significance criteria used in paper: greater than 2-fold change (|LFC|>=1.0) and Padj<0.01

gene	dysregulated by OE of	LFC
Rv3031/-	Rv0818/glnR	-1.05
Rv3031/-	Rv3223c/sigH	-1.19
Rv3031/-	Rv0023/-	-1.37
Rv3031/-	Rv2034/-	-1.38
Rv3031/-	Rv0022c/whiB5	-1.39
Rv3031/-	Rv2506/-	-1.5
Rv3031/-	Rv3286c/sigF	-1.56
Rv3031/-	Rv0576/-	-1.6

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Not upregulated by other genes.
Downregulates:
- Does not downregulate other genes.
Downregulated by:

Property	Value	Creator	Evidence	PMID	Comment
Name	Putative branching enzyme involved in methylglucose lipolysaccharide synthesis	mjackson	ISS		Other (lipo)polysaccharides [Methylglucose lipolysaccharides, glycogen and capsular alpha-1,4 glucan]
Citation	Genetic basis for the biosynthesis of methylglucose lipopolysaccharides in Mycobacterium tuberculosis. G. Stadthagen, T. Sambou et al. J. Biol. Chem. 2007	mjackson		17640872	Putative branching enzyme involved in methylglucose lipolysaccharide synthesis
Other	TBPWY:(MGLP and alpha-1,4 glucans)	mjackson			Putative branching enzyme involved in methylglucose lipolysaccharide synthesis G. Stadthagen, T. Sambou et al. Genetic basis for the biosynthesis of methylglucose lipopolysaccharides in Mycobacterium tuberculosis. J. Biol. Chem. 2007
Citation	Polymethylated polysaccharides from Mycobacterium species revisited. authors,M. Jackson,PJ. Brennan J. Biol. Chem. 2009	mjackson		18786916	Putative branching enzyme involved in methylglucose lipolysaccharide synthesis
Other	TBPWY:(MGLP and alpha-1,4 glucans)	mjackson			Putative branching enzyme involved in methylglucose lipolysaccharide synthesis authors,M. Jackson,PJ. Brennan Polymethylated polysaccharides from Mycobacterium species revisited. J. Biol. Chem. 2009

TB Genome Annotation Portal