Rv1461 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: Fe-S cluster assembly protein SufB
- REFSEQ: hypothetical protein
- PATRIC: Iron-sulfur cluster assembly protein SufB @ intein-containing
- TUBERCULIST: Conserved protein
- NCBI: hypothetical protein
- updated information (H37Rv4):
  - gene name: sufB/pps1
  - function: assembly of iron-sulfur clusters
  - reference: (Huet 2005, PMID: 16109955)
Type: Essential
Start: 1646989
End: 1649529
Operon:

Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
- GO:0090305 - nucleic acid phosphodiester bond hydrolysis (Uniprot)
- GO:0040007 - growth (Uniprot)
- GO:0016787 - hydrolase activity (Uniprot)
- GO:0016539 - intein-mediated protein splicing (Uniprot)
- GO:0016226 - iron-sulfur cluster assembly (Uniprot)
- GO:0006314 - intron homing (Uniprot)
- GO:0005829 - cytosol (Uniprot)
- GO:0005515 - protein binding (Uniprot)
- GO:0004519 - endonuclease activity (Uniprot)
- GO:0004518 - nuclease activity (Uniprot)
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): (none with >35% aa id)
Links to additional information on Rv1461:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -7.788 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MTLTPEASKSVAQPPTQAPLTQEEAIASLGRYGYGWADSDVAGANAQRGLSEAVVRDISAKKNEPDWMLQSRLKALRIFDRKPIPKWGSNLDGIDFDNIK
YFVRSTEKQAASWDDLPEDIRNTYDRLGIPEAEKQRLVAGVAAQYESEVVYHQIREDLEAQGVIFLDTDTGLREHPDIFKEYFGTVIPAGDNKFSALNTA
VWSGGSFIYVPPGVHVDIPLQAYFRINTENMGQFERTLIIADEGSYVHYVEGCLPAGELITTADGDLRPIESIRVGDFVTGHDGRPHRVTAVQVRDLDGE
LFTFTPMSPANAFSVTAEHPLLAIPRDEVRVMRKERNGWKAEVNSTKLRSAEPRWIAAKDVAEGDFLIYPKPKPIPHRTVLPLEFARLAGYYLAEGHACL
TNGCESLIFSFHSDEFEYVEDVRQACKSLYEKSGSVLIEEHKHSARVTVYTKAGYAAMRDNVGIGSSNKKLSDLLMRQDETFLRELVDAYVNGDGNVTRR
NGAVWKRVHTTSRLWAFQLQSILARLGHYATVELRRPGGPGVIMGRNVVRKDIYQVQWTEGGRGPKQARDCGDYFAVPIKKRAVREAHEPVYNLDVENPD
SYLAYGFAVHNCTAPIYKSDSLHSAVVEIIVKPHARVRYTTIQNWSNNVYNLVTKRARAEAGATMEWIDGNIGSKVTMKYPAVWMTGEHAKGEVLSVAFA
GEDQHQDTGAKMLHLAPNTSSNIVSKSVARGGGRTSYRGLVQVNKGAHGSRSSVKCDALLVDTVSRSDTYPYVDIREDDVTMGHEATVSKVSENQLFYLM
SRGLTEDEAMAMVVRGFVEPIAKELPMEYALELNRLIELQMEGAVG

(Nucleotide sequence available on KEGG)

Additional Information

sufB or pps1 - assembly of iron-sulfur clusters.

Huet G, Daffé M, Saves I. Identification of the Mycobacterium
tuberculosis SUF machinery as the exclusive mycobacterial system of
[Fe-S] cluster assembly: evidence for its implication in the
pathogen's survival. J Bacteriol. 2005 Sep;187(17):6137-46. doi:
10.1128/JB.187.17.6137-6146.2005. PMID: 16109955; PMCID: PMC1196142.

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
Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 59 non-insertions in a row out of 59 sites
Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 59 non-insertions in a row out of 59 sites
Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 1.000000; 59 non-insertions in a row out of 59 sites
Essential	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 59 non-insertions in a row out of 59 sites
Essential	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 1.000000; 59 non-insertions in a row out of 59 sites
Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 0.02
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)

Binds To:
- No bindings to other targets were found.
Bound By:
- No bindings from other targets were found.

Interactions based on ChIPSeq data (Minch et al. 2014)

Binds To:
- No bindings to other targets were found.
Bound By:
- Rv0967 (csoR) (Direct binding)
- Rv1816 (-) (Direct binding)
- Rv0691c (-) (Upstream of operon)
- Rv1033c (trcR) (Upstream of operon)
- Rv1460 (-) (Upstream of operon)
- Rv2610c (pimA) (Upstream of operon)

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:
- Not downregulated by other genes.

Property	Value	Creator	Evidence	PMID	Comment
Interaction	PhysicalInteraction Rv1463	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) authors,G. Huet,M. Daff,I. Saves Identification of the Mycobacterium tuberculosis SUF machinery as the exclusive mycobacterial system of [Fe-S] cluster assembly: evidence for its implication in the pathogen's survival. J. Bacteriol. 2005
Interaction	Regulatory Rv1464	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) authors,G. Huet,JP. Castaing,D. Fournier,M. Daff,I. Saves Protein splicing of SufB is crucial for the functionality of the Mycobacterium tuberculosis SUF machinery. J. Bacteriol. 2006
Interaction	PhysicalInteraction Rv1462	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) authors,G. Huet,M. Daff,I. Saves Identification of the Mycobacterium tuberculosis SUF machinery as the exclusive mycobacterial system of [Fe-S] cluster assembly: evidence for its implication in the pathogen's survival. J. Bacteriol. 2005
Interaction	PhysicalInteraction Rv1463	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) B. Murugasu-Oei, A. Tay et al. Upregulation of stress response genes and ABC transporters in anaerobic stationary-phase Mycobacterium smegmatis. Mol. Gen. Genet. 1999
Citation	Identification of the Mycobacterium tuberculosis SUF machinery as the exclusive mycobacterial system of [Fe-S] cluster assembly: evidence for its implication in the pathogen's survival. authors,G. Huet,M. Daff,I. Saves J. Bacteriol. 2005	vijayachitra	IPI	16109955	Yeast two-hybrid (Physical interaction)
Interaction	Regulatory Rv1462	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) authors,G. Huet,M. Daff,I. Saves Identification of the Mycobacterium tuberculosis SUF machinery as the exclusive mycobacterial system of [Fe-S] cluster assembly: evidence for its implication in the pathogen's survival. J. Bacteriol. 2005
Interaction	Regulatory Rv1463	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) authors,G. Huet,M. Daff,I. Saves Identification of the Mycobacterium tuberculosis SUF machinery as the exclusive mycobacterial system of [Fe-S] cluster assembly: evidence for its implication in the pathogen's survival. J. Bacteriol. 2005
Interaction	Regulatory Rv1464	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) authors,G. Huet,M. Daff,I. Saves Identification of the Mycobacterium tuberculosis SUF machinery as the exclusive mycobacterial system of [Fe-S] cluster assembly: evidence for its implication in the pathogen's survival. J. Bacteriol. 2005
Citation	Protein splicing of SufB is crucial for the functionality of the Mycobacterium tuberculosis SUF machinery. authors,G. Huet,JP. Castaing,D. Fournier,M. Daff,I. Saves J. Bacteriol. 2006	vijayachitra	IPI	16621837	Yeast two-hybrid (Physical interaction)
Interaction	Regulatory Rv1462	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) authors,G. Huet,JP. Castaing,D. Fournier,M. Daff,I. Saves Protein splicing of SufB is crucial for the functionality of the Mycobacterium tuberculosis SUF machinery. J. Bacteriol. 2006
Interaction	Regulatory Rv1463	vijayachitra	IPI		Yeast two-hybrid (Physical interaction) authors,G. Huet,JP. Castaing,D. Fournier,M. Daff,I. Saves Protein splicing of SufB is crucial for the functionality of the Mycobacterium tuberculosis SUF machinery. J. Bacteriol. 2006
Interaction	RegulatedBy Rv0348	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.. B. Abomoelak, EA. Hoye et al. mosR, a novel transcriptional regulator of hypoxia and virulence in Mycobacterium tuberculosis. J. Bacteriol. 2009
Interaction	RegulatedBy Rv3557c	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 Rv1931c	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 Rv1359	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 Rv0818	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
Interaction	RegulatedBy Rv0260c	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

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