Rv1404 (-)

Current annotations:
- TBCAP: (community-based annotations - see table at bottom of page)
- TBDB: hypothetical protein
- REFSEQ: transcriptional regulatory protein
- PATRIC: Transcriptional regulator MarR family
- TUBERCULIST: Probable transcriptional regulatory protein
- NCBI: Probable transcriptional regulatory protein
- updated information (H37Rv4):
  - gene name: -
  - function:
  - reference:
Type: Not Target
Start: 1580591
End: 1581073
Operon:

Trans-membrane region:
Role: I.J.1 - Repressors/activators
GO terms:
- GO:0044212 - transcription regulatory region DNA binding (Uniprot)
- GO:0006355 - regulation of transcription, DNA-templated (Uniprot)
- GO:0006351 - transcription, DNA-templated (Uniprot)
- GO:0005886 - plasma membrane (Uniprot)
- GO:0003700 - DNA binding transcription factor activity (Uniprot)
- GO:0003677 - DNA binding (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: 2nyx
Search for Homologs in PDB

Top 10 Homologs in PDB (as of Nov 2020):

PDB	aa ident	species	PDB title
2NYX	100%	Mycobacterium tuberculosis	Crystal structure of RV1404 from Mycobacterium tuberculosis
4XRF	36%	Bacillus cereus (strain ATCC 14579 / DSM 31)	Crystal structure of MepR like protein complexed with pseudoligands

Links to additional information on Rv1404:
- TBDB (updated)
- Phyre2 structure prediction, model: final.casp.pdb (from Mao et al, 2013)
- UniProt
- AlphaFold model
- Vulnerability = -0.916 (from Jeremy Rock's lab)
- KEGG - nucleotide and amino acid sequences of gene
- Mycobrowser
- PATRIC
- BioCyc
- Systems Biology

Amino Acid Sequence

MMPTEYPATAEESVDVITDALLTASRLLVAISAHSIAQVDENITIPQFRTLVILSNHGPINLATLATLLGVQPSATGRMVDRLVGAELIDRLPHPTSRRE
LLAALTKRGRDVVRQVTEHRRTEIARIVEQMAPAERHGLVRALTAFTEAGGEPDARYEIE

(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
Non-Essential	Sodium Oleate	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 2 non-insertions in a row out of 7 sites
Non-Essential	Lignoceric Acid	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 7 sites
Non-Essential	Phosphatidylcholine	H37RvMA	Gumbel	Subhalaxmi Nambi	Probability of Essentiality: 0.000000; 3 non-insertions in a row out of 7 sites
Uncertain	minimal media + 0.1% glycerol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.244100; 6 non-insertions in a row out of 8 sites
Uncertain	minimal media + 0.01% cholesterol	H37RvMA	Gumbel	Griffin et al. (2011)	Probability of Essentiality: 0.984500; 7 non-insertions in a row out of 8 sites
Non-Essential	7H10-glycerol	H37RvMA	TraSH	Sassetti et al. (2003a)
Non-Essential	C57BL/6J mice (8 weeks)	H37RvMA	TraSH	Sassetti et al. (2003b)	Hybridization Ratio: 2.71
Non-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

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

Binds To:
- Rv0011c (-) (Direct binding)
- Rv0012 (-) (Direct binding)
- Rv0054 (ssb) (Direct binding)
- Rv0195 (-) (Direct binding)
- Rv0244c (fadE5) (Direct binding)
- Rv0469 (umaA) (Direct binding)
- Rv0576 (-) (Direct binding)
- Rv0694 (lldD1) (Direct binding)
- Rv0746 (PE_PGRS9) (Direct binding)
- Rv0747 (PE_PGRS10) (Direct binding)
- Rv0783c (emrB) (Direct binding)
- Rv0850 (-) (Direct binding)
- Rv1094 (desA2) (Direct binding)
- Rv1116 (-) (Direct binding)
- Rv1139c (-) (Direct binding)
- Rv1256c (cyp130) (Direct binding)
- Rv1306 (atpF) (Direct binding)
- Rv1336 (cysM) (Direct binding)
- Rv1374c (-) (Direct binding)
- Rv1375 (-) (Direct binding)
- Rv1386 (PE15) (Direct binding)
- Rv1392 (metK) (Direct binding)
- Rv1403c (-) (Direct binding)
- Rv1404 (-) (Direct binding)
- Rv1405c (-) (Direct binding)
- Rv1406 (fmt) (Direct binding)
- Rv1441c (PE_PGRS26) (Direct binding)
- Rv1442 (bisC) (Direct binding)
- Rv1682 (-) (Direct binding)
- Rv1730c (-) (Direct binding)
- Rv1731 (gabD2) (Direct binding)
- Rv2198c (mmpS3) (Direct binding)
- Rv2390c (-) (Direct binding)
- Rv2408 (PE24) (Direct binding)
- Rv2549c (vapC20) (Direct binding)
- Rv2550c (vapB20) (Direct binding)
- Rv2551c (-) (Direct binding)
- Rv2956 (-) (Direct binding)
- Rv3018A (PE27A) (Direct binding)
- Rv3324c (moaC3) (Direct binding)
- Rv3370c (dnaE2) (Direct binding)
- Rv3532 (PPE61) (Direct binding)
- Rv3573c (fadE34) (Direct binding)
- Rv3574 (kstR) (Direct binding)
- Rv3746c (PE34) (Direct binding)
- Rv3747 (-) (Direct binding)
- Rv3812 (PE_PGRS62) (Direct binding)
- Rv3822 (-) (Direct binding)
- Rv3863 (-) (Direct binding)
- Rv0013 (trpG) (Upstream of operon)
- Rv0577 (TB27.3) (Upstream of operon)
- Rv1137c (-) (Upstream of operon)
- Rv1138c (-) (Upstream of operon)
- Rv1255c (-) (Upstream of operon)
- Rv1376 (-) (Upstream of operon)
- Rv1387 (PPE20) (Upstream of operon)
- Rv1407 (fmu) (Upstream of operon)
- Rv1408 (rpe) (Upstream of operon)
- Rv1409 (ribG) (Upstream of operon)
- Rv2197c (-) (Upstream of operon)
- Rv2389c (rpfD) (Upstream of operon)
- Rv3322c (-) (Upstream of operon)
- Rv3323c (moaX) (Upstream of operon)
Bound By:
- Rv0081 (-) (Direct binding)
- Rv0967 (csoR) (Direct binding)
- Rv1033c (trcR) (Direct binding)
- Rv1353c (-) (Direct binding)
- Rv1404 (-) (Direct binding)

Property	Value	Creator	Evidence	PMID	Comment
Interaction	Regulatory Rv3532	raj252000	IEP		Co-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
Interaction	Regulatory Rv3533c	salluamity1	IEP		Co-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
Interaction	Regulatory Rv3533c	salluamity1	IEP		Co-expression (Functional linkage) MI. Voskuil,D. Schnappinger,R. Rutherford,Y. Liu,GK. Schoolnik Regulation of the Mycobacterium tuberculosis PE/PPE genes. Tuberculosis (Edinb) 2004
Interaction	Regulatory Rv3531c	raj252000	IEP		Co-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
Interaction	Regulatory Rv3531c	raj252000	IEP		Co-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
Interaction	PhysicalInteraction Rv1931c	swatigandhi19	IMP		Co-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
Interaction	PhysicalInteraction Rv1931c	swatigandhi19	IMP		Co-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
Interaction	Regulatory Rv1403c	ashwinigbhat	IEP		qRT-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
Interaction	Regulatory Rv1405c	ashwinigbhat	IEP		qRT-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
Citation	IdeR in mycobacteria: from target recognition to physiological function. S. Ranjan, S. Yellaboina et al. Crit. Rev. Microbiol. 2006	ashwinigbhat	TAS	16809230	positional relative entropy method
Interaction	Regulatory Rv2711	ashwinigbhat	TAS		positional relative entropy method S. Ranjan, S. Yellaboina et al. IdeR in mycobacteria: from target recognition to physiological function. Crit. Rev. Microbiol. 2006
Citation	Computational 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 2005	ashwinigbhat	TAS	15746274	positional relative entropy method
Interaction	Regulatory Rv2711	ashwinigbhat	TAS		positional 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
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	ashwinigbhat	IEP	18985025	Microarray analysis
Interaction	Regulatory Rv1931c	ashwinigbhat	IEP		Microarray analysis G. Balzsi, AP. Heath et al. The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. Mol. Syst. Biol. 2008
Citation	Characterization of two in vivo-expressed methyltransferases of the Mycobacterium tuberculosis complex: antigenicity and genetic regulation. P. Golby, J. Nunez et al. Microbiology (Reading, Engl.) 2008	ashwinigbhat	IEP	18375799	qRT-PCR
Interaction	Transcription Rv0193c	sourish10	IMP		Protein-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
Interaction	Regulatory Rv0195	aparna.vchalam	IEP		Co-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
Interaction	RegulatedBy Rv1931c	yamir.moreno	ISO		E.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
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	ISO	18985025	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv1404	yamir.moreno	ISO		E.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
Interaction	RegulatedBy Rv1404	yamir.moreno	ISO		E.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
Citation	The temporal response of the Mycobacterium tuberculosis gene regulatory network during growth arrest. G. Balzsi, AP. Heath et al. Mol. Syst. Biol. 2008	yamir.moreno	ISO	18985025	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv1931c	yamir.moreno	ISO		E.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
Interaction	RegulatedBy Rv1931c	yamir.moreno	ISO		E.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
Citation	Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006	yamir.moreno	ISO	16530225	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv1404	yamir.moreno	ISO		E.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
Interaction	RegulatedBy Rv1404	yamir.moreno	ISO		E.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
Citation	Evolutionary dynamics of prokaryotic transcriptional regulatory networks. authors,M. Madan Babu,SA. Teichmann,L. Aravind J. Mol. Biol. 2006	yamir.moreno	ISO	16530225	E.coli orthology based inference. Orthologous pair regulator-target found in E.coli.
Interaction	Regulates Rv1931c	yamir.moreno	ISO		E.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

TB Genome Annotation Portal

Rv1404 (-)

Amino Acid Sequence

Additional Information

Gene interactions based on ChIPSeq and Transcription Factor Over-Expression (TFOE) (Systems Biology)

Interactions based on ChIPSeq data

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

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

TBCAP

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