Rv1385 (pyrF)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: orotidine 5'-phosphate decarboxylase
- REFSEQ: orotidine 5'-phosphate decarboxylase
- PATRIC: Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23)
- TUBERCULIST: Probable orotidine 5'-phosphate decarboxylase PyrF (OMP decarboxylase) (ompdecase)
- NCBI: Probable orotidine 5'-phosphate decarboxylase PyrF (OMP decarboxylase) (ompdecase)
- updated information (H37Rv4):
  - gene name: pyrF
  - function:
  - reference:
Type: Not Target
Start: 1560445
End: 1561269
Operon:

Trans-membrane region:
Role: I.F.2 - Pyrimidine ribonucleotide biosynthesis
GO terms:
- GO:0044205 - 'de novo' UMP biosynthetic process (Uniprot)
- GO:0016831 - carboxy-lyase activity (Uniprot)
- GO:0016829 - lyase activity (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0006221 - pyrimidine nucleotide biosynthetic process (Uniprot)
- GO:0006207 - 'de novo' pyrimidine nucleobase biosynthetic process (Uniprot)
- GO:0004590 - orotidine-5'-phosphate decarboxylase activity (Uniprot)
- GO:0003824 - catalytic activity (Uniprot)
Reaction(s) (based on iSM810 metabolic model):
- OMP[c] -> CO2[c] + UMP[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
3V75	52%	Streptomyces avermitilis	Crystal structure of putative orotidine 5'-phosphate decarboxylase from Streptomyces avermitilis ma-4680
3QW4	37%	Leishmania donovani	Structure of Leishmania donovani UMP synthase
3QW3	37%	Leishmania infantum	Structure of Leishmania donovani OMP decarboxylase

Links to additional information on pyrF:
- 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 = -7.577 (from Jeremy Rock's lab)

Amino Acid Sequence

VTGFGLRLAEAKARRGPLCLGIDPHPELLRGWDLATTADGLAAFCDICVRAFADFAVVKPQVAFFESYGAAGFAVLERTIAELRAADVLVLADAKRGDIG
ATMSAYATAWVGDSPLAADAVTASPYLGFGSLRPLLEVAAAHGRGVFVLAATSNPEGAAVQNAAADGRSVAQLVVDQVGAANEAAGPGPGSIGVVVGATA
PQAPDLSAFTGPVLVPGVGVQGGRPEALGGLGGAASSQLLPAVAREVLRAGPGVPELRAAGERMRDAVAYLAAV

(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: 0.875100; 6 non-insertions in a row out of 6 sites
Uncertain	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.961450; 6 non-insertions in a row out of 6 sites
Uncertain	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.973250; 6 non-insertions in a row out of 6 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.946150; 6 non-insertions in a row out of 7 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.946850; 6 non-insertions in a row out of 7 sites
No-Data	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Too-Short	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: -1
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:
- Rv0023 (-)

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:
- Not upregulated by other genes.
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0023 (-)

TB Genome Annotation Portal