Rv3484 (cpsA)
Current annotations:
TBCAP: (community-based annotations - see table at bottom of page )
TBDB: hypothetical protein
REFSEQ: hypothetical protein
PATRIC: Cell envelope-associated transcriptional attenuator LytR-CpsA-Psr subfamily A1 (as in PMID19099556)
TUBERCULIST: Possible conserved protein CpsA
NCBI: Possible conserved protein CpsA
updated information (H37Rv4):
gene name: cpsA
function:
reference:
Coordinates in H37Rv: 3903078 - 3904616
Gene length: 1539 bp (with stop codon), 512 aa (without stop codon)
Operon:
Trans-membrane region:
Role: V - Conserved hypotheticals
GO terms:
Reaction(s) (based on iSM810 metabolic model):
Gene Expression Profile Gene Modules Orthologs among selected mycobacteria Protein structure:
Search for Latest Homologs in PDB Top 10 Homologs in PDB (as of Apr 2026): (none with >35% aa id)
Links to additional information on cpsA:
Amino Acid Sequence
MARSEGNRPRHRAVPQPSRIRKRLSRGVMTLVSVVALLMTGAGYWVAHGALGGITISQALTPEDPRSSGNNMNILLIGLDSRKDQEGNDLPWSVLKQLHA
GDSDDGGYNTNTLILVHVGADGKVVAFSIPRDDWVPFTGVPGYNHIKIKEAYGLTKQYVAEQLANQGVSDRKELETRGREAARAATLRAVRSLTGVPIDY
FAEINLAGFYDLAQTLGGVDVCLNHAVYDSYSGADFPAGRQRLNAAQALAFVRQRHGLDNGDLDRTHRQQAFLSSVMRELQDSGTFTNLDRLDNLMAVAR
KDVVLSAGWDEDLFRRMGDLAGGNVEFRTLPVVRYDNIDGQDVNIIDPTAIRAEVAAAFGSAPPTSQTAAAAKPNPSTVVDVVNAGSISGLASQVSGALL
KRGYTAGQVRDRESGDPFTTAIEYGAGAETDAQNVADLLGIDAPNHPDPAVAPGHIRVTVDTNFSLPAPDEATAAATSTETSTYPLYGGGTTTDPTPDQG
APIDGGGVPCVN
(
Nucleotide sequence available on
KEGG )
Additional Information
MtbTnDB - interactive tool for exploring a database of published TnSeq datasets for Mtb
TnSeqCorr
Rv3484/cpsA,
gene len: 1538 bp, num TA sites: 28
condition dataset call medium method notes
in-vitro DeJesus 2017 mBio growth advantage 7H9 HMM fully saturated, 14 TnSeq libraries combined
in-vitro Sassetti 2003 Mol Micro non-essential 7H9 TRASH essential if hybridization ratio<0.2
in-vivo (mice) Sassetti 2003 PNAS essential BL6 mice TRASH essential if hybridization ratio<0.4, min over 4 timepoints (1-8 weeks)
in-vitro (glycerol) Griffin 2011 PPath non-essential M9 minimal+glycerol Gumbel 2 replicates; Padj<0.05
in-vitro (cholesterol) Griffin 2011 PPath non-essential M9 minimal+cholesterol Gumbel 3 replicates; Padj<0.05
differentially essential in cholesterol Griffin 2011 PPath YES (LFC=4.12) cholesterol vs glycerol resampling-SR YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in cholesterol
in-vitro Smith 2022 eLife growth defect 7H9 HMM 6 replicates (raw data in Subramaniam 2017, PMID 31752678)
in-vivo (mice) Smith 2022 eLife growth defect BL6 mice HMM 6 replicates (raw data in Subramaniam 2017, PMID 31752678)
differentially essential in mice Smith 2022 eLife YES (LFC=-3.954) in-vivo vs in-vitro ZINB YES if Padj<0.05, else not significant; LFC<0 means less insertions/more essential in mice
in-vitro (minimal) Minato 2019 mSys non-essential minimal medium HMM
in-vitro (YM rich medium) Minato 2019 mSys non-essential YM rich medium HMM 7H9 supplemented with ~20 metabolites (amino acids, cofactors)
differentially essential in YM rich medium Minato 2019 mSys YES (LFC=1.22) YM rich vs minimal medium resampling
Analysis of Positive Selection in Clinical Isolates
*new*
data from Culviner et al (2025) (55,259 Mtb clinical isolates)
overall pN/pS for Rv3484: 0.541443543
lineage-specific pN/pS in L1: 0.412297435
lineage-specific pN/pS in L2: 0.466288766
lineage-specific pN/pS in L3: 0.526745516
lineage-specific pN/pS in L4: 0.625736778
Analysis of dN/dS (omega) in a global collection of 10k Mtb clinical isolates using GenomegaMap (Window model)
clinical isolates collection: global set of 10,626 Mtb genomes
In the omega plots, the black line shows the mean estimate of omega (dN/dS) at each codon, and the blue lines are the bounds for the 95% credible interval (95%CI, from MCMC sampling).
A gene is under significant positive selection if the lower-bound of the 95%CI of omega (lower blue line) exceeds 1.0 at any codon.
global set of 10,626 Mtb clinical isolates
under significant positive selection? NO
omega peak height (95%CI lower bound) 1.17 (0.47)
codons under selection
omega plots
genetic variants* link
* example format for variants: "D27 (GAC): D27H (CAC,11)" means "Asp27 (native codon GAC) mutated to His (codon CAC) in 11 isolates"
TnSeq Data No data currently available.
No TnSeq data currently available for this Target.
RNASeq Data No data currently available.
BioCyc
Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology )
NOTE:
see table of TFOE interactions below
Interactions based on ChIPSeq data
Binds To:
No bindings to other targets were found.
Bound By:
Binds To:
No bindings to other targets were found.
Bound By:
No bindings to other targets were found.
TFOE = Transcription Factor Over-Expression study
significance criteria used in paper: greater than 2-fold change (|LFC|>=1.0) and Padj<0.01
gene dysregulated by OE of LFC
Rv3484/cpsA Rv0081/- 1.36
Rv3484/cpsA Rv3849/espR -1.05
Upregulates:
Does not upregulate other genes.
Upregulated by:
Downregulates:
Does not downregulate other genes.
Downregulated by:
