TB Genome Annotation Portal

Rv3601c (panD)

Amino Acid Sequence

MLRTMLKSKIHRATVTCADLHYVGSVTIDADLMDAADLLEGEQVTIVDIDNGARLVTYAITGERGSGVIGINGAAAHLVHPGDLVILIAYATMDDARART
YQPRIVFVDAYNKPIDMGHDPAFVPENAGELLDPRLGVG
(Nucleotide sequence available on KEGG)

Additional Information
















Analysis of Positive Selection in Clinical Isolates
*new*






Moldova (2,057)global set (5,195)

under significant positive selection?NONO

omega peak height (95%CI lower bound)0.55 (0.01)1.67 (0.54)

codons under selection

omega plots

genetic variants*linklink

statistics at each codonlinklink



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











    ESSENTIALITY 

    







    



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


TnSeqCorr - genes with correlated TnSeq profiles across ~100 conditions

Rv3601c/panD,
gene len: 419 bp, num TA sites: 10



conditiondatasetcallmediummethodnotes

in-vitroDeJesus 2017 mBioessential7H9HMMfully saturated, 14 TnSeq libraries combined

in-vitroSassetti 2003 Mol Microno data 7H9TRASHessential if hybridization ratio<0.2

in-vivo (mice)Sassetti 2003 PNASno data BL6 miceTRASHessential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)

in-vitro (glycerol)Griffin 2011 PPathessentialM9 minimal+glycerolGumbel2 replicates; Padj<0.05

in-vitro (cholesterol)Griffin 2011 PPathessentialM9 minimal+cholesterolGumbel3 replicates; Padj<0.05

differentially essential in cholesterol Griffin 2011 PPathNO (LFC=0.0)cholesterol vs glycerolresampling-SRYES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol

in-vitroSmith 2022 eLifeessential7H9HMM6 replicates (raw data in Subramaniam 2017, PMID 31752678)

in-vivo (mice)Smith 2022 eLifeessentialBL6 miceHMM6 replicates (raw data in Subramaniam 2017, PMID 31752678)

differentially essential in miceSmith 2022 eLifeNO (LFC=0.0)in-vivo vs in-vitroZINBYES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice

in-vitro (minimal)Minato 2019 mSysessentialminimal mediumHMM

in-vitro (YM rich medium)Minato 2019 mSysnon-essentialYM rich mediumHMM7H9 supplemented with ~20 metabolites (amino acids, vitamins)

differentially essential in YM rich mediumMinato 2019 mSysYES (LFC=4.26)YM rich vs minimal mediumresampling







    












 





    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
    

    
    

    
    
    

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    • Binds To:
      
    
        

            
      •  No bindings to other targets were found.

    
      
    
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    • Bound By:
      
    
    
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    Interactions based on ChIPSeq data (Minch et al. 2014)
    




    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:
      
    


    








    

    






    


    


    


    TBCAP
    
Tubculosis Community Annotation Project (    Slayden et al., 2013)
    
Rv3601c (panD)

    

    PropertyValueCreatorEvidencePMIDComment
    
InteractionRegulatedBy Rv0981yamir.morenoIEPMicroarrays. 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..
    H. He, R. Hovey et al. MprAB is a stress-responsive two-component system that directly regulates expression of sigma factors SigB and SigE in Mycobacterium tuberculosis. J. Bacteriol. 2006
    
Citation3-Fluoroaspartate and pyruvoyl-dependant aspartate decarboxylase: exploiting the unique characteristics of fluorine to probe reactivity and binding. authors,J. de Villiers,L. Koekemoer,E. Strauss Chemistry 2010jevans20645337Not inhibited by fluorinated substrate analogues
    
CitationA pantothenate auxotroph of Mycobacterium tuberculosis is highly attenuated and protects mice against tuberculosis. authors,VK. Sambandamurthy,X. Wang,B. Chen,RG. Russell,S. Derrick,FM. Collins,SL. Morris,WR. Jacobs Nat. Med. 2002jjmcfadden12219086Inferred from direct assay
    
TermEC:4.1.1.11 Aspartate 1-decarboxylase. - NRjjmcfaddenNRInferred from direct assay
    authors,VK. Sambandamurthy,X. Wang,B. Chen,RG. Russell,S. Derrick,FM. Collins,SL. Morris,WR. Jacobs A pantothenate auxotroph of Mycobacterium tuberculosis is highly attenuated and protects mice against tuberculosis. Nat. Med. 2002
    

    


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