Rv0244c (fadE5)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: acyl-CoA dehydrogenase fadE5
- REFSEQ: acyl-CoA dehydrogenase FADE5
- PATRIC: acyl-CoA dehydrogenase
- TUBERCULIST: Probable acyl-CoA dehydrogenase FadE5
- NCBI: Probable acyl-CoA dehydrogenase FadE5
- updated information (H37Rv4):
  - gene name: fadE5
  - function:
  - reference:
Type: Conditional
Start: 293798
End: 295633
Operon:

Trans-membrane region:
Role: I.A.3 - Fatty acids
GO terms:
- GO:0055114 - oxidation-reduction process (Uniprot)
- GO:0052572 - response to host immune response (Uniprot)
- GO:0050660 - flavin adenine dinucleotide binding (Uniprot)
- GO:0016627 - oxidoreductase activity, acting on the CH-CH group of donors (Uniprot)
- GO:0016491 - oxidoreductase activity (Uniprot)
- GO:0008152 - metabolic process (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0005576 - extracellular region (Uniprot)
- GO:0006979 - response to oxidative stress (FLUTE) (FLUTE Assigned!Y2 report, Nambi et al.)
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):

PDB	aa ident	species	PDB title
6KSE	99%	Mycobacterium tuberculosis	Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria tuberculosisin complex with C18CoA
6KSB	81%	Mycobacterium smegmatis	Crystal Structure of E447A M130G Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C16CoA
6KRI	81%	Mycobacterium smegmatis	Crystal Structure of Acyl-CoA Dehydrogenase FadE5 from Mycobacteria smegmatis with product released
6KPT	81%	Mycobacterium smegmatis	Crystal Structure of Acyl-CoA Dehydrogenase FadE5 from Mycobacteria smegmatis
6LQ7	81%	Mycobacterium smegmatis	Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C17CoA
6LQ6	81%	Mycobacterium smegmatis	Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C20CoA
6LQ5	81%	Mycobacterium smegmatis	Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C16CoA
6LQ4	81%	Mycobacterium smegmatis	Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C14CoA
6LQ3	81%	Mycobacterium smegmatis	Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C12CoA
6LQ2	81%	Mycobacterium smegmatis	Crystal Structure of E447A Acyl-CoA Dehydrogenase FadE5 mutant from Mycobacteria smegmatis in complex with C10CoA

Links to additional information on fadE5:
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = 0.492 (from Jeremy Rock's lab)
- BioCyc
- Systems Biology

Amino Acid Sequence

VSHYRSNVRDQVFNLFEVLGVDKALGHGEFSDVDVDTARDMLAEVSRLAEGPVAESFVEGDRNPPVFDPKTHSVMLPESFKKSVNAMLEAGWDKVGIDEA
LGGMPMPKAVVWALHEHILGANPAVWMYAGGAGFAQILYHLGTEEQKKWAVLAAERGWGSTMVLTEPDAGSDVGAARTKAVQQADGSWHIDGVKRFITSG
DSGDLFENIFHLVLARPEGAGPGTKGLSLYFVPKFLFDVETGEPGERNGVFVTNVEHKMGLKVSATCELAFGQHGVPAKGWLVGEVHNGIAQMFEVIEQA
RMMVGTKAIATLSTGYLNALQYAKSRVQGADLTQMTDKTAPRVTITHHPDVRRSLMTQKAYAEGLRALYLYTATFQDAAVAEVVHGVDAKLAVKVNDLML
PVVKGVGSEQAYAKLTESLQTLGGSGFLQDYPIEQYIRDAKIDSLYEGTTAIQAQDFFFRKIVRDKGVALAHVSGQIQEFVDSGAGNGRLKTERALLAKA
LTDVQGMAAALTGYLMAAQQDVTSLYKVGLGSVRFLMSVGDLIIGWLLQRQAAVAVAALDAGATGDERSFYEGKVAVASFFAKNFLPLLTSTREVIETLD
NDIMELDEAAF

(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: 0.754000; 9 non-insertions in a row out of 23 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 23 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 23 sites
Non-Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.000000; 1 non-insertions in a row out of 23 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.771650; 7 non-insertions in a row out of 23 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
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:
- Rv0023 (-) (Direct binding)
- Rv0047c (-) (Direct binding)
- Rv0678 (-) (Direct binding)
- Rv0691c (-) (Direct binding)
- Rv0818 (-) (Direct binding)
- Rv1033c (trcR) (Direct binding)
- Rv1404 (-) (Direct binding)
- Rv2034 (-) (Direct binding)
- Rv2989 (-) (Direct binding)
- Rv3597c (lsr2) (Direct binding)

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

Upregulates:
- Does not upregulate other genes.
Upregulated by:
- Rv0023 (-)
- Rv0081 (-)
Downregulates:
- Does not downregulate other genes.
Downregulated by:
- Rv0324 (-)
- Rv0818 (-)

Property	Value	Creator	Evidence	Comment
Interaction	RegulatedBy Rv0182c	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.. JH. Lee, DE. Geiman et al. Role of stress response sigma factor SigG in Mycobacterium tuberculosis. J. Bacteriol. 2008
Interaction	RegulatedBy Rv3744	yamir.moreno	IDA	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv3416	yamir.moreno	IDA	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv2034	yamir.moreno	IDA	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009
Interaction	RegulatedBy Rv0445c	yamir.moreno	IDA	One hybrid reporter system. Physical binding of the regulator to the regulated promoter proved by using electrophoretic mobility shift assay. . M. Guo, H. Feng et al. Dissecting transcription regulatory pathways through a new bacterial one-hybrid reporter system. Genome Res. 2009

TB Genome Annotation Portal