Rv2835c (ugpA)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: sn-glycerol 3-phosphate transporter permease
- REFSEQ: sn-glycerol-3-phosphate transport integral membrane protein ABC transporter UGPA
- PATRIC: Glycerol-3-phosphate ABC transporter permease protein UgpA (TC 3.A.1.1.3)
- TUBERCULIST: Probable Sn-glycerol-3-phosphate transport integral membrane protein ABC transporter UgpA
- NCBI: Probable Sn-glycerol-3-phosphate transport integral membrane protein ABC transporter UgpA
- updated information (H37Rv4):
  - gene name: ugpA
  - function:
  - reference:
Type: Not Target
Start: 3141311
End: 3142222
Operon:

Trans-membrane region:
Role: III.A.3 - Carbohydrates, organic acids and alcohols
GO terms:
- GO:0055085 - transmembrane transport (Uniprot)
- GO:0016021 - integral component of membrane (Uniprot)
- GO:0016020 - membrane (Uniprot)
- GO:0005887 - integral component of plasma membrane (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): (none with >35% aa id)
Links to additional information on ugpA:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.92 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MAAPQRARLRSSKERVRDYALFVVLVGPNVALLLLFVYRPLADNIRLSFFDWNVSDPSARFVGLSNYTEWFTRSDTRQIVFNTAVFTGAAVVGSMVLGLA
LAMLLDRPLRGRNLVRSTVFAPFVISGAAVGLAAQFVFDPHFGLIQDLLRRIGVGVPDFYQDARWALFMVTITYVWKNLGYTFVIYLAALQGVRRDLLEA
AEIDGASRWAVFRRVLLPQLRPTTFFLSITVLINSLQVFDVINVMTRGGPEGTGTTTMVYQVYVETFRNFRAGYGATVATIMFLVLLAVTYYQVRVMDRG
QRQ

(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: 0.722800; 7 non-insertions in a row out of 16 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 16 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 16 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.001250; 5 non-insertions in a row out of 16 sites
Non-Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 16 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: 0.94
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:

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:
- Rv0757 (phoP)
- Rv0818 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Not downregulated by other genes.

TBCAP

Tubculosis Community Annotation Project (

Slayden et al., 2013

Rv2835c (ugpA)

Property	Value	Creator	Evidence	PMID	Comment
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
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
Interaction	Regulatory Rv0616c	akankshajain.21	IEP		Co-expression (Functional linkage) T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003
Interaction	RegulatedBy Rv0491	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.. T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003

Property

Value

Creator

Evidence

PMID

Comment

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

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

Term

TBRXN:GLYC3Pabc sn-Glycerol 3-phosphate transport via ABC system - ISS

njamshidi

ISS

12657046

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

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

Interaction

Regulatory Rv0616c

akankshajain.21

IEP

Co-expression (Functional linkage)
T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003

Interaction

RegulatedBy Rv0491

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..
T. Parish, DA. Smith et al. The senX3-regX3 two-component regulatory system of Mycobacterium tuberculosis is required for virulence. Microbiology (Reading, Engl.) 2003

Comments