RegulonDB

RegulonDB RegulonDB 11.0: Gene Form

rpmE gene in Escherichia coli K-12 genome

Gene local context to scale (view description)

Gene
Name:	rpmE
Synonym(s):	ECK3928, EG10889, b3936
Genome position(nucleotides):	4127013 --> 4127225
Strand:	forward
Sequence:	Get nucleotide sequence FastaFormat
GC content %:	49.3
External database links:

ASAP:	ABE-0012867
CGSC:	237
ECHOBASE:	EB0882
ECOLIHUB:	rpmE
OU-MICROARRAY:	b3936
STRING:	511145.b3936
COLOMBOS:	rpmE

Product

Name:

50S ribosomal subunit protein L31

Synonym(s):

RpmE

Sequence:

Get amino acid sequence Fasta Format

Cellular location:

cytosol,ribosome

Molecular weight:

7.871

Isoelectric point:

9.867

Motif(s):

Type	Positions	Sequence	Comment
	1 -> 65	MKKDIHPKYEEITASCSCGNVMKIRSTVGHDLNLDVCSKCHPFFTGKQRDVATGGRVDRFNKRFN
	16 -> 16	C	UniProt: No Zn(2+) binding..
	18 -> 18	C	UniProt: Binds Zn(2+) normally..
	37 -> 40	CSKC	UniProt: Binds Zn(2+) normally..

Classification:

Multifun Terms (GenProtEC)
		2 - information transfer --> 2.3 - protein related --> 2.3.2 - translation
		2 - information transfer --> 2.3 - protein related --> 2.3.8 - ribosomal proteins
		6 - cell structure --> 6.6 - ribosomes
Gene Ontology Terms (GO)
	cellular_component	GO:0005737 - cytoplasm GO:0005829 - cytosol GO:0005840 - ribosome GO:0022625 - cytosolic large ribosomal subunit
	molecular_function	GO:0003735 - structural constituent of ribosome GO:0046872 - metal ion binding GO:0003723 - RNA binding GO:0019843 - rRNA binding GO:0008270 - zinc ion binding
	biological_process	GO:1904689 - negative regulation of cytoplasmic translational initiation GO:0006412 - translation GO:0006413 - translational initiation GO:0002181 - cytoplasmic translation

Note(s):

Note(s): ...[more].

Reference(s):

[1] Dabbs ER. 1981
[2] Eckert I., et al., 2020
[3] Klebl DP., et al., 2020
[4] Mustoe AM., et al., 2018

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SMR:

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Operon

Name:

rpmE

Operon arrangement:

Transcription unit	Promoter
rpmE	rpmEp1
rpmE	rpmEp2

RNA cis-regulatory element

Attenuation:	Translational

Elements in the selected gene context region unrelated to any object in RegulonDB

	Type	Name	Post Left	Post Right	Strand	Notes	Evidence (Confirmed, Strong, Weak)	References
	promoter	TSS_4640	4126911		forward	nd	[RS-EPT-CBR]	[5]
	promoter	TSS_4641	4126913		forward	nd	[RS-EPT-CBR]	[5]

Evidence
[RS-EPT-CBR] RNA-seq using two enrichment strategies for primary transcripts and consistent biological replicates

Reference(s)
[1] Dabbs ER., 1981, The gene for ribosomal protein L31, rpmE, is located at 88.5 minutes on the Escherichia coli chromosomal linkage map., J Bacteriol 148(1):379-82
[2] Eckert I., Weinberg Z., 2020, Discovery of 20 novel ribosomal leader candidates in bacteria and archaea., BMC Microbiol 20(1):130
[3] Klebl DP., Gravett MSC., Kontziampasis D., Wright DJ., Bon RS., Monteiro DCF., Trebbin M., Sobott F., White HD., Darrow MC., Thompson RF., Muench SP., 2020, Need for Speed: Examining Protein Behavior during CryoEM Grid Preparation at Different Timescales., Structure 28(11):1238-1248.e4
[4] Mustoe AM., Busan S., Rice GM., Hajdin CE., Peterson BK., Ruda VM., Kubica N., Nutiu R., Baryza JL., Weeks KM., 2018, Pervasive Regulatory Functions of mRNA Structure Revealed by High-Resolution SHAPE Probing., Cell 173(1):181-195.e18
[5] Salgado H, Peralta-Gil M, Gama-Castro S, Santos-Zavaleta A, Muñiz-Rascado L, García-Sotelo JS, Weiss V, Solano-Lira H, Martínez-Flores I, Medina-Rivera A, Salgado-Osorio G, Alquicira-Hernández S, Alquicira-Hernández K, López-Fuentes A, Porrón-Sotelo L, Huerta AM, Bonavides-Martínez C, Balderas-Martínez YI, Pannier L, Olvera M, Labastida A, Jiménez-Jacinto V, Vega-Alvarado L, Del Moral-Chávez V, Hernández-Alvarez A, Morett E, Collado-Vides J., 2012, RegulonDB v8.0: omics data sets, evolutionary conservation, regulatory phrases, cross-validated gold standards and more., Nucleic Acids Res.

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