TB Genome Annotation Portal

Rv1404 (-)

Amino Acid Sequence

MMPTEYPATAEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRE
LLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLVRALTAFTEAGGEPDARYEIE
(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)1.19 (0.08)0.82 (0.25)

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

Rv1404/-,
gene len: 482 bp, num TA sites: 8



conditiondatasetcallmediummethodnotes

in-vitroDeJesus 2017 mBionon-essential7H9HMMfully saturated, 14 TnSeq libraries combined

in-vitroSassetti 2003 Mol Micronon-essential 7H9TRASHessential if hybridization ratio<0.2

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

in-vitro (glycerol)Griffin 2011 PPathuncertainM9 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=-1.64)cholesterol vs glycerolresampling-SRYES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol

in-vitroSmith 2022 eLifenon-essential7H9HMM6 replicates (raw data in Subramaniam 2017, PMID 31752678)

in-vivo (mice)Smith 2022 eLifenon-essentialBL6 miceHMM6 replicates (raw data in Subramaniam 2017, PMID 31752678)

differentially essential in miceSmith 2022 eLifeNO (LFC=-0.636)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 mSysnon-essentialminimal mediumHMM

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

differentially essential in YM rich mediumMinato 2019 mSysNO (LFC=-0.88)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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    Interactions based on ChIPSeq data (Minch et al. 2014)
    




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














    

    






    


    


    


    TBCAP
    
Tubculosis Community Annotation Project (    Slayden et al., 2013)
    
Rv1404 (-)

    

    PropertyValueCreatorEvidencePMIDComment
    
InteractionRegulatory Rv3532raj252000IEPCo-expression (Functional linkage)
    P. Golby, J. Nunez et al. Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. Microbiology (Reading, Engl.) 2008
    
InteractionRegulatory Rv3533csalluamity1IEPCo-expression (Functional linkage)
    P. Golby, J. Nunez et al. Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. Microbiology (Reading, Engl.) 2008
    
InteractionRegulatory Rv3533csalluamity1IEPCo-expression (Functional linkage)
    MI. Voskuil,D. Schnappinger,R. Rutherford,Y. Liu,GK. Schoolnik Regulation of the Mycobacterium tuberculosis PE/PPE genes. Tuberculosis (Edinb) 2004
    
InteractionRegulatory Rv3531craj252000IEPCo-expression (Functional linkage)
    SL. Kendall, M. Withers et al. A highly conserved transcriptional repressor controls a large regulon involved in lipid degradation in Mycobacterium smegmatis and Mycobacterium tuberculosis. Mol. Microbiol. 2007
    
InteractionRegulatory Rv3531craj252000IEPCo-expression (Functional linkage)
    P. Golby, J. Nunez et al. Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. Microbiology (Reading, Engl.) 2008
    
InteractionPhysicalInteraction Rv1931cswatigandhi19IMPCo-expression (Functional Linkage)
    G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
    
InteractionPhysicalInteraction Rv1931cswatigandhi19IMPCo-expression (Functional Linkage)
    CC. Frota, KG. Papavinasasundaram et al. The AraC family transcriptional regulator Rv1931c plays a role in the virulence of Mycobacterium tuberculosis. Infect. Immun. 2004
    
InteractionRegulatory Rv1403cashwinigbhatIEPqRT-PCR
    P. Golby, J. Nunez et al. Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. Microbiology (Reading, Engl.) 2008
    
InteractionRegulatory Rv1405cashwinigbhatIEPqRT-PCR
    P. Golby, J. Nunez et al. Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. Microbiology (Reading, Engl.) 2008
    
CitationIdeR in mycobacteria: from target recognition to physiological function. S. Ranjan, S. Yellaboina et al. Crit. Rev. Microbiol. 2006ashwinigbhatTAS16809230positional relative entropy method
    
InteractionRegulatory Rv2711ashwinigbhatTASpositional relative entropy method
    S. Ranjan, S. Yellaboina et al. IdeR in mycobacteria: from target recognition to physiological function. Crit. Rev. Microbiol. 2006
    
CitationComputational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames. P. Prakash, S. Yellaboina et al. Bioinformatics 2005ashwinigbhatTAS15746274positional relative entropy method
    
InteractionRegulatory Rv2711ashwinigbhatTASpositional relative entropy method
    P. Prakash, S. Yellaboina et al. Computational prediction and experimental verification of novel IdeR binding sites in the upstream sequences of Mycobacterium tuberculosis open reading frames. Bioinformatics 2005
    
CitationThe temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008ashwinigbhatIEP18985025Microarray analysis
    
InteractionRegulatory Rv1931cashwinigbhatIEPMicroarray analysis
    G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
    
CitationCharacterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. P. Golby, J. Nunez et al. Microbiology (Reading, Engl.) 2008ashwinigbhatIEP18375799qRT-PCR
    
InteractionTranscription Rv0193csourish10IMPProtein-Protein
    P. Golby, J. Nunez et al. Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. Microbiology (Reading, Engl.) 2008
    
InteractionRegulatory Rv0195aparna.vchalamIEPCo-expression (Functional linkage)
    P. Golby, J. Nunez et al. Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. Microbiology (Reading, Engl.) 2008
    
InteractionRegulatedBy Rv1931cyamir.morenoISOE.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
    
CitationThe temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008yamir.morenoISO18985025E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    
InteractionRegulates Rv1404yamir.morenoISOE.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
    
InteractionRegulatedBy Rv1404yamir.morenoISOE.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
    
CitationThe temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008yamir.morenoISO18985025E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    
InteractionRegulates Rv1931cyamir.morenoISOE.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
    
InteractionRegulatedBy Rv1931cyamir.morenoISOE.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
    
CitationEvolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006yamir.morenoISO16530225E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    
InteractionRegulates Rv1404yamir.morenoISOE.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
    
InteractionRegulatedBy Rv1404yamir.morenoISOE.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
    
CitationEvolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006yamir.morenoISO16530225E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    
InteractionRegulates Rv1931cyamir.morenoISOE.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
    authors,M. Madan Babu,SA. Teichmann,L. Aravind Evolutionary dynamics of prokaryotic transcriptional regulatory networks. J. Mol. Biol. 2006
    

    


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