Rv2833c (ugpB)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: sn-glycerol 3-phosphate transporter substrate-binding protein
- REFSEQ: sn-glycerol-3-phosphate-binding lipoprotein UGPB
- PATRIC: Glycerol-3-phosphate ABC transporter periplasmic glycerol-3-phosphate-binding protein (TC 3.A.1.1.3)
- TUBERCULIST: Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB
- NCBI: Probable Sn-glycerol-3-phosphate-binding lipoprotein UgpB
- updated information (H37Rv4):
  - gene name: ugpB
  - function:
  - reference:
Type: Not Target
Start: 3139174
End: 3140484
Operon:

Trans-membrane region:
Role: III.A.3 - Carbohydrates, organic acids and alcohols
GO terms:
- GO:0040007 - growth (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- PI[c] -> GL3P[c]
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):

PDB	aa ident	species	PDB title
6R1B	100%	Mycobacterium tuberculosis	Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine
6R1B	100%	Mycobacterium tuberculosis	Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine
4MFI	100%	Mycobacterium tuberculosis	Crystal structure of Mycobacterium tuberculosis UgpB
6R1B	96%	Mycobacterium tuberculosis	Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine
6R1B	96%	Mycobacterium tuberculosis	Crystal structure of UgpB from Mycobacterium tuberculosis in complex with glycerophosphocholine

Links to additional information on ugpB:
- 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 = 0.997 (from Jeremy Rock's lab)

Amino Acid Sequence

MDPLNRRQFLALAAAAAGVTAGCAGMGGGGSVKSGSGPIDFWSSHPGQSSAAERELIGRFQDRFPTLSVKLIDAGKDYDEVAQKFNAALIGTDVPDVVLL
DDRWWFHFALSGVLTALDDLFGQVGVDTTDYVDSLLADYEFNGRHYAVPYARSTPLFYYNKAAWQQAGLPDRGPQSWSEFDEWGPELQRVVGAGRSAHGW
ANADLISWTFQGPNWAFGGAYSDKWTLTLTEPATIAAGNFYRNSIHGKGYAAVANDIANEFATGILASAVASTGSLAGITASARFDFGAAPLPTGPDAAP
ACPTGGAGLAIPAKLSEERKVNALKFIAFVTNPTNTAYFSQQTGYLPVRKSAVDDASERHYLADNPRARVALDQLPHTRTQDYARVFLPGGDRIISAGLE
SIGLRGADVTKTFTNIQKRLQVILDRQIMRKLAGHG

(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
Uncertain	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.980000; 11 non-insertions in a row out of 19 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 19 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 19 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 5 non-insertions in a row out of 19 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 4 non-insertions in a row out of 19 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.16
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

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0818 (-)

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

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

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0818 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Term	TBRXN:GLYC3Pabc sn-Glycerol 3-phosphate transport via ABC system - ISS	njamshidi	ISS	12657046	Believed to be importer exp evidence PMID: 12657046. See also PMID: 10978546. Cole et al: Tuberculosis and the Tubercle Bacillus chapter 24 - unknown mechism. high affinity for basic amino acids; unknown mechanism, for current version assume permease/diffusion transport authors,CM. Sassetti,DH. Boyd,EJ. Rubin Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003
Citation	The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis. authors,M. Braibant,P. Gilot,J. Content FEMS Microbiol. Rev. 2000	njamshidi	ISS	10978546\|12657046	Believed to be importer exp evidence PMID: 12657046. See also PMID: 10978546. Cole et al: Tuberculosis and the Tubercle Bacillus chapter 24 - unknown mechism. high affinity for basic amino acids; unknown mechanism, for current version assume permease/diffusion transport
Term	TBRXN:GLYC3Pabc sn-Glycerol 3-phosphate transport via ABC system - ISS	njamshidi	ISS	12657046	Believed to be importer exp evidence PMID: 12657046. See also PMID: 10978546. Cole et al: Tuberculosis and the Tubercle Bacillus chapter 24 - unknown mechism. high affinity for basic amino acids; unknown mechanism, for current version assume permease/diffusion transport authors,M. Braibant,P. Gilot,J. Content The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis. FEMS Microbiol. Rev. 2000
Citation	Genes required for mycobacterial growth defined by high density mutagenesis. authors,CM. Sassetti,DH. Boyd,EJ. Rubin Mol. Microbiol. 2003	njamshidi	IPI	12657046	Believed to be importer exp evidence PMID: 12657046. See also PMID: 10978546. Cole et al: Tuberculosis and the Tubercle Bacillus chapter 24 - unknown mechism. high affinity for basic amino acids; unknown mechanism, for current version assume permease/diffusion transport
Term	TBRXN:GLYC3Pabc sn-Glycerol 3-phosphate transport via ABC system - IPI	njamshidi	IPI	12657046	Believed to be importer exp evidence PMID: 12657046. See also PMID: 10978546. Cole et al: Tuberculosis and the Tubercle Bacillus chapter 24 - unknown mechism. high affinity for basic amino acids; unknown mechanism, for current version assume permease/diffusion transport authors,CM. Sassetti,DH. Boyd,EJ. Rubin Genes required for mycobacterial growth defined by high density mutagenesis. Mol. Microbiol. 2003
Citation	The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis. authors,M. Braibant,P. Gilot,J. Content FEMS Microbiol. Rev. 2000	njamshidi	IPI	10978546\|12657046	Believed to be importer exp evidence PMID: 12657046. See also PMID: 10978546. Cole et al: Tuberculosis and the Tubercle Bacillus chapter 24 - unknown mechism. high affinity for basic amino acids; unknown mechanism, for current version assume permease/diffusion transport
Term	TBRXN:GLYC3Pabc sn-Glycerol 3-phosphate transport via ABC system - IPI	njamshidi	IPI	12657046	Believed to be importer exp evidence PMID: 12657046. See also PMID: 10978546. Cole et al: Tuberculosis and the Tubercle Bacillus chapter 24 - unknown mechism. high affinity for basic amino acids; unknown mechanism, for current version assume permease/diffusion transport authors,M. Braibant,P. Gilot,J. Content The ATP binding cassette (ABC) transport systems of Mycobacterium tuberculosis. FEMS Microbiol. Rev. 2000
Citation	Genes required for mycobacterial growth defined by high density mutagenesis. authors,CM. Sassetti,DH. Boyd,EJ. Rubin Mol. Microbiol. 2003	njamshidi	ISS	12657046	Believed to be importer exp evidence PMID: 12657046. See also PMID: 10978546. Cole et al: Tuberculosis and the Tubercle Bacillus chapter 24 - unknown mechism. high affinity for basic amino acids; unknown mechanism, for current version assume permease/diffusion transport
Symbol	UgpB	jlew			Contains a functional tat sequence. Test for functional tat sequences using a BlaC reporter. 13 identified. JA. McDonough, JR. McCann et al. Identification of functional Tat signal sequences in Mycobacterium tuberculosis proteins. J. Bacteriol. 2008
Citation	Identification of functional Tat signal sequences in Mycobacterium tuberculosis proteins. JA. McDonough, JR. McCann et al. J. Bacteriol. 2008	jlew		18658266	Contains a functional tat sequence. Test for functional tat sequences using a BlaC reporter. 13 identified.

TB Genome Annotation Portal