TB Genome Annotation Portal

Rv2461c (clpP1)

Amino Acid Sequence

VSQVTDMRSNSQGLSLTDSVYERLLSERIIFLGSEVNDEIANRLCAQILLLAAEDASKDISLYINSPGGSISAGMAIYDTMVLAPCDIATYAMGMAASMG
EFLLAAGTKGKRYALPHARILMHQPLGGVTGSAADIAIQAEQFAVIKKEMFRLNAEFTGQPIERIEADSDRDRWFTAAEALEYGFVDHIITRAHVNGEAQ
(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: 0.991550;
10 non-insertions in a row out of 10 sites		
            



            

                Uncertain
                Lignoceric Acid
                H37RvMA

                    Gumbel



                    Subhalaxmi Nambi


                Probability of Essentiality: 0.978900;
7 non-insertions in a row out of 10 sites		
            



            

                Essential
                Phosphatidylcholine
                H37RvMA

                    Gumbel



                    Subhalaxmi Nambi


                Probability of Essentiality: 0.999450;
10 non-insertions in a row out of 10 sites		
            



            

                Essential
                minimal media + 0.1% glycerol
                H37RvMA

                    Gumbel



                    Griffin et al. (2011)


                Probability of Essentiality: 0.998950;
10 non-insertions in a row out of 10 sites		
            



            

                Essential
                minimal media + 0.01% cholesterol
                H37RvMA

                    Gumbel



                    Griffin et al. (2011)


                Probability of Essentiality: 0.999000;
10 non-insertions in a row out of 10 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
    


    

    

    

    
    


                
    
                    
    
                    RNA processing and modification
                
    

                
    
                    
    
                    Energy production and conversion
                
    

                
    
                    
    
                    Chromatin structure and dynamics
                
    

                
    
                    
    
                    Amino acid transport and metabolism
                
    

                
    
                    
    
                    Cell cycle control, cell division, chromosome partitioning
                
    

                
    
                    
    
                    Carbohydrate transport and metabolism
                
    

                
    
                    
    
                    Nucleotide transport and metabolism
                
    

                
    
                    
    
                    Lipid transport and metabolism
                
    

                
    
                    
    
                    Coenzyme transport and metabolism
                
    

                
    
                    
    
                    Transcription
                
    

                
    
                    
    
                    Translation, ribosomal structure and biogenesis
                
    

                
    
                    
    
                    Cell wall/membrane/envelope biogenesis
                
    

                
    
                    
    
                    Replication, recombination and repair
                
    

                
    
                    
    
                    Posttranslational modification, protein turnover, chaperones
                
    

                
    
                    
    
                    Cell motility
                
    

                
    
                    
    
                    Secondary metabolites biosynthesis, transport and catabolism
                
    

                
    
                    
    
                    Inorganic ion transport and metabolism
                
    

                
    
                    
    
                    Function unknown
                
    

                
    
                    
    
                    General function prediction only
                
    

                
    
                    
    
                    Intracellular trafficking, secretion, and vesicular transport
                
    

                
    
                    
    
                    Signal transduction mechanisms
                
    

                
    
                    
    
                    Extracellular structures
                
    

                
    
                    
    
                    Defense mechanisms
                
    

                
    
                    
    
                    Nuclear structure
                
    

                
    
                    
    
                    Cytoskeleton
                
    


    
    
    
  • BioCyc

                    Co-regulated genes based on gene expression profiling (Systems Biology, Inferelator Network)
                
    • 

                
    
                    
                    Differentially expressed as result of RNASeq in glycerol environment (Only top 20 genes shown sorted by log fold change with p_adj 0.05). 
                
    

                
    
                    
                    Conditionally essential as result of TNSeq (Only top 20 genes shown sorted by log fold change with p_adj 0.05). 
                
    

                
    
                    
                
  • BioCyc

                    Transcription factor binding based on ChIP-Seq (Systems Biology)
                
    • 


    
    

    






    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)
    
Rv2461c (clpP1)

    

    PropertyValueCreatorEvidencePMIDComment
    
CitationClgR regulation of chaperone and protease systems is essential for Mycobacterium tuberculosis parasitism of the macrophage. authors,M. Estorninho,H. Smith,J. Thole,J. Harders-Westerveen,A. Kierzek,RE. Butler,O. Neyrolles,GR. Stewart Microbiology (Reading, Engl.) 2010akankshajain.21IEP20688819Co-expression (Functional linkage)
    
InteractionRegulatory Rv2475cakankshajain.21IEPCo-expression (Functional linkage)
    authors,M. Estorninho,H. Smith,J. Thole,J. Harders-Westerveen,A. Kierzek,RE. Butler,O. Neyrolles,GR. Stewart ClgR regulation of chaperone and protease systems is essential for Mycobacterium tuberculosis parasitism of the macrophage. Microbiology (Reading, Engl.) 2010
    
InteractionPhysicalInteraction Rv2457cakankshajain.21IDAStructural analysis
    AK. Gupta, VM. Katoch et al. Microarray analysis of efflux pump genes in multidrug-resistant Mycobacterium tuberculosis during stress induced by common anti-tuberculous drugs. Microb. Drug Resist. 2010
    
CitationInsights into the inter-ring plasticity of caseinolytic proteases from the X-ray structure of Mycobacterium tuberculosis ClpP1. H. Ingvarsson, MJ. Mat et al. Acta Crystallogr. D Biol. Crystallogr. 2007akankshajain.21IDA17242518Structural analysis
    
InteractionPhysicalInteraction Rv2460cakankshajain.21IDAStructural analysis
    H. Ingvarsson, MJ. Mat et al. Insights into the inter-ring plasticity of caseinolytic proteases from the X-ray structure of Mycobacterium tuberculosis ClpP1. Acta Crystallogr. D Biol. Crystallogr. 2007
    
InteractionPhysicalInteraction Rv2457cakankshajain.21IDAStructural analysis
    H. Ingvarsson, MJ. Mat et al. Insights into the inter-ring plasticity of caseinolytic proteases from the X-ray structure of Mycobacterium tuberculosis ClpP1. Acta Crystallogr. D Biol. Crystallogr. 2007
    
CitationThe ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. authors,A. Gribun,MS. Kimber,R. Ching,R. Sprangers,KM. Fiebig,WA. Houry J. Biol. Chem. 2005akankshajain.21IDA15701650Structural analysis
    
InteractionPhysicalInteraction Rv2460cakankshajain.21IDAStructural analysis
    authors,A. Gribun,MS. Kimber,R. Ching,R. Sprangers,KM. Fiebig,WA. Houry The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. J. Biol. Chem. 2005
    
InteractionPhysicalInteraction Rv2457cakankshajain.21IDAStructural analysis
    authors,A. Gribun,MS. Kimber,R. Ching,R. Sprangers,KM. Fiebig,WA. Houry The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. J. Biol. Chem. 2005
    
CitationClpP: a distinctive family of cylindrical energy-dependent serine proteases. authors,AY. Yu,WA. Houry FEBS Lett. 2007richasinha4uIDA17499722Spectrophotometric Analysis
    
InteractionRegulatory Rv2457crichasinha4uIDASpectrophotometric Analysis
    authors,AY. Yu,WA. Houry ClpP: a distinctive family of cylindrical energy-dependent serine proteases. FEBS Lett. 2007
    
CitationSequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli. authors,MR. Maurizi,WP. Clark,Y. Katayama,S. Rudikoff,J. Pumphrey,B. Bowers,S. Gottesman J. Biol. Chem. 1990richasinha4uIDA2197275Structural Analysis
    
InteractionRegulatory Rv2457crichasinha4uIDAStructural Analysis
    authors,MR. Maurizi,WP. Clark,Y. Katayama,S. Rudikoff,J. Pumphrey,B. Bowers,S. Gottesman Sequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli. J. Biol. Chem. 1990
    
CitationThe ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate. authors,S. Gottesman,WP. Clark,MR. Maurizi J. Biol. Chem. 1990richasinha4uIDA2186030Structural Analysis
    
InteractionRegulatory Rv2457crichasinha4uIDAStructural Analysis
    authors,S. Gottesman,WP. Clark,MR. Maurizi The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate. J. Biol. Chem. 1990
    
CitationClpP: a distinctive family of cylindrical energy-dependent serine proteases. authors,AY. Yu,WA. Houry FEBS Lett. 2007richasinha4uIDA17499722Structural Analysis
    
InteractionRegulatory Rv2457crichasinha4uIDAStructural Analysis
    authors,AY. Yu,WA. Houry ClpP: a distinctive family of cylindrical energy-dependent serine proteases. FEBS Lett. 2007
    
CitationMicroarray analysis of efflux pump genes in multidrug-resistant Mycobacterium tuberculosis during stress induced by common anti-tuberculous drugs. AK. Gupta, VM. Katoch et al. Microb. Drug Resist. 2010akankshajain.21IDA20001742Structural analysis
    
InteractionPhysicalInteraction Rv2460cakankshajain.21IDAStructural analysis
    AK. Gupta, VM. Katoch et al. Microarray analysis of efflux pump genes in multidrug-resistant Mycobacterium tuberculosis during stress induced by common anti-tuberculous drugs. Microb. Drug Resist. 2010
    
InteractionPhysicalInteraction Rv2460cakankshajain.21IDAStructural analysis
    authors,A. Gribun,MS. Kimber,R. Ching,R. Sprangers,KM. Fiebig,WA. Houry The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. J. Biol. Chem. 2005
    
CitationSequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli. authors,MR. Maurizi,WP. Clark,Y. Katayama,S. Rudikoff,J. Pumphrey,B. Bowers,S. Gottesman J. Biol. Chem. 1990richasinha4uIDA2197275Spectrophotometric Analysis
    
InteractionRegulatory Rv2457crichasinha4uIDASpectrophotometric Analysis
    authors,MR. Maurizi,WP. Clark,Y. Katayama,S. Rudikoff,J. Pumphrey,B. Bowers,S. Gottesman Sequence and structure of Clp P, the proteolytic component of the ATP-dependent Clp protease of Escherichia coli. J. Biol. Chem. 1990
    
CitationThe ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate. authors,S. Gottesman,WP. Clark,MR. Maurizi J. Biol. Chem. 1990richasinha4uIDA2186030Spectrophotometric Analysis
    
InteractionRegulatory Rv2457crichasinha4uIDASpectrophotometric Analysis
    authors,S. Gottesman,WP. Clark,MR. Maurizi The ATP-dependent Clp protease of Escherichia coli. Sequence of clpA and identification of a Clp-specific substrate. J. Biol. Chem. 1990
    
InteractionPhysicalInteraction Rv2457crichasinha4uIDAStructural Analysis
    authors,B. Banecki,A. Wawrzynow,J. Puzewicz,C. Georgopoulos,M. Zylicz Structure-function analysis of the zinc-binding region of the Clpx molecular chaperone. J. Biol. Chem. 2001
    
InteractionPhysicalInteraction Rv2457crichasinha4uIDAStructural Analysis
    authors,LW. Donaldson,U. Wojtyra,WA. Houry Solution structure of the dimeric zinc binding domain of the chaperone ClpX. J. Biol. Chem. 2003
    
InteractionPhysicalInteraction Rv2457crichasinha4uIDAStructural Analysis
    authors,AY. Yu,WA. Houry ClpP: a distinctive family of cylindrical energy-dependent serine proteases. FEBS Lett. 2007
    
InteractionPhysicalInteraction Rv2460cakankshajain.21IDAStructural analysis
    AK. Gupta, VM. Katoch et al. Microarray analysis of efflux pump genes in multidrug-resistant Mycobacterium tuberculosis during stress induced by common anti-tuberculous drugs. Microb. Drug Resist. 2010
    
InteractionPhysicalInteraction Rv2457cvmevada102ISOStructural analysis
    authors,A. Gribun,MS. Kimber,R. Ching,R. Sprangers,KM. Fiebig,WA. Houry The ClpP double ring tetradecameric protease exhibits plastic ring-ring interactions, and the N termini of its subunits form flexible loops that are essential for ClpXP and ClpAP complex formation. J. Biol. Chem. 2005
    
InteractionPhysicalInteraction Rv2457crichasinha4uIDASpectrophotometric Analysis
    authors,B. Banecki,A. Wawrzynow,J. Puzewicz,C. Georgopoulos,M. Zylicz Structure-function analysis of the zinc-binding region of the Clpx molecular chaperone. J. Biol. Chem. 2001
    
InteractionPhysicalInteraction Rv2457crichasinha4uIDASpectrophotometric Analysis
    authors,LW. Donaldson,U. Wojtyra,WA. Houry Solution structure of the dimeric zinc binding domain of the chaperone ClpX. J. Biol. Chem. 2003
    
InteractionPhysicalInteraction Rv2457crichasinha4uIDASpectrophotometric Analysis
    authors,AY. Yu,WA. Houry ClpP: a distinctive family of cylindrical energy-dependent serine proteases. FEBS Lett. 2007
    
InteractionPhysicalInteraction Rv2457cvmevada102ISOStructural analysis
    AK. Gupta, VM. Katoch et al. Microarray analysis of efflux pump genes in multidrug-resistant Mycobacterium tuberculosis during stress induced by common anti-tuberculous drugs. Microb. Drug Resist. 2010
    

    


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