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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	rplF
Gene Synonym(s)	ECK3292, b3305, JW3267^[1], JW3267
Product Desc.	50S ribosomal subunit protein L6^[2]^[3]; Component of 50S ribosomal subunit^[3]; ribosome^[2]^[3] 50S ribosomal subunit protein L6; gentamicin sensitivity^[4]
Product Synonyms(s)	50S ribosomal subunit protein L6^[1], B3305^[2]^[1], RplF^[2]^[1] , ECK3292, JW3267, b3305
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ^[2], rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-prlA-rpmJ
Regulation/Activity
Quick Links
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</protect> See Help:Quickview for help with entering information in the Quickview table. <protect></protect>

Notes

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Gene

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Nomenclature

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See Help:Gene_nomenclature for help with entering information in the Gene Nomenclature table.

Standard name	rplF
Mnemonic	Ribosomal protein, large
Synonyms	ECK3292, b3305, JW3267^[1], JW3267
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Notes

Location(s) and DNA Sequence

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<protect> See Help:Gene_location for help entering information in the Gene Location and DNA sequence table.

Strain	Map location	Genome coordinates	Genome browsers	Sequence links
MG1655	74.22 minutes	MG1655: 3444162..3443629 <gbrowseImage> name=NC_000913:3443629..3444162 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3374045..3373512 <gbrowseImage> name=NC_012967:3373512..3374045 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3330786..3331319 <gbrowseImage> name=NC_012759:3330786..3331319 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4194276..4194809 <gbrowseImage> name=NC_007779:4194276..4194809 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3541907..3541374 <gbrowseImage> name=NC_010473:3541374..3541907 source=DH10B preset=GeneLocation </gbrowseImage>	GBrowse(DH10B)	FASTA Dump
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Notes

Sequence Features

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See Help:Gene_sequence_features for help in entering sequence features in EcoliWiki.

Feature Type	Strain	Genomic Location	Evidence	Reference	Notes
Coding Start (SO:0000323)	MG1655	3443632	Edman degradation	PMID:791672 PMID:9298646
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Notes

Alleles and Phenotypes

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See Help:Gene_alleles for how to enter or edit alleles and phenotypes in EcoliWiki.

Allele	Nt change(s)	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Availability	Comments
rplF15		amino acids 152 to 177 replaced by Ala-Leu	Resistant to	(in gentamicin resistant strain: GS50-15), table 4	PMID:342908	Strain: GS50-15	~~Strain variation~~; seeded from UniProt:P0AG55 127.0.0.1The annotation as natural variants is wrong; this strain was selected as a GmR mutant.
rplF8		amino acids 158 – 177 replaced by Thr-Leu	Resistant to	(in gentamicin resistant strain: GS20-8)	PMID:342908		Strain variation; seeded from UniProt:P0AG55
rplF8	7-nt insertion at nucleotide 2722, which introduces a frameshift and a premature stop codon	amino acid residues 158 to 177 replaced by Thr-Leu	Resistant to	gentamycin resistant, table 4	PMID:342908	Strain: GE20-8	sequence: ^[5]
rplF10			Resistant to	gentamycin resistant	PMID:342908	Strain: GE20-10	Table 4
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Notes

Genetic Interactions

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Interactor	Interaction	Allele	Score(s)	Reference(s)	Accessions	Notes
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Notes

Genetic Resources

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See Help:Gene_resources for help entering information into the Genetic Resources table.

Resource	Resource Type	Source	Notes/Reference
JW3267	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCTCGTGTTGCTAAAGCACC Primer 2:CCtTTCTTCTTAGCCTCTTTGGT
E1H9	Kohara Phage	Genobase	PMID:3038334
smg-3082::Tn10	Linked marker	CAG12071 = CGSC7444^[6]	est. P1 cotransduction: 59% ^[7] Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
zhf-3084::Tn10	Linked marker	CAG18456 = CGSC7576^[6]	est. P1 cotransduction: 5% ^[7] Synonyms:zhe-3084::Tn10nnnCAG18456 also carries cysG0 (CGSC).
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10869	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10869	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000860	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947803	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0862	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010827	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Product(s)

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Nomenclature

See Help:Product_nomenclature for help entering or editing information in this section of EcoliWiki.

Standard name	RplF
Synonyms	50S ribosomal subunit protein L6^[1], B3305^[2]^[1], RplF^[2]^[1] , ECK3292, JW3267, b3305
Product description	50S ribosomal subunit protein L6^[2]^[3]; Component of 50S ribosomal subunit^[3]; ribosome^[2]^[3] 50S ribosomal subunit protein L6; gentamicin sensitivity^[4]
EC number (for enzymes)
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Notes

Function

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<protect> Gene Ontology
See Help:Gene_ontology for help entering or editing GO terms and GO annotations in EcoliWiki.

Qualifier	GO ID	GO term name	Reference	Evidence Code	with/from	Aspect	Notes	Status
	GO:0003723	RNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0694	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003735	structural constituent of ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000702	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003735	structural constituent of ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002358	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003735	structural constituent of ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019906	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003735	structural constituent of ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005840	ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000702	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005840	ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002358	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005840	ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019906	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005840	ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020040	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005840	ribosome	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0689	C	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01365	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000702	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR002358	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019906	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020040	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019843	rRNA binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01365	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019843	rRNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR000702	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019843	rRNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019906	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019843	rRNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR020040	F	Seeded from EcoCyc (v14.0)	complete
	GO:0019843	rRNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0699	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030529	ribonucleoprotein complex	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0687	C	Seeded from EcoCyc (v14.0)	complete
	GO:0046677	response to antibiotic	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0046	P	Seeded from EcoCyc (v14.0)	complete
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Interactions See Help:Product_interactions for help entering or editing information about gene product interactions in this section of EcoliWiki.

Partner Type	Partner	Notes	References	Evidence
Protein	Subunits of 50S ribosomal subunit	could be indirect
Protein	plsB		PMID:16606699	Experiment(s):EBI-1145494
Protein	rplB		PMID:16606699	Experiment(s):EBI-1145494
Protein	mdtC		PMID:16606699	Experiment(s):EBI-1145494
Protein	Subunits of ribosome	could be indirect
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Notes

Localization

See Help:Product_localization for how to add or edit information in this section of EcoliWiki.

Compartment	Description	Evidence	Reference/Source	Notes
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Notes

Structure and Physical Properties

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<protect> Physical Properties See Help:Product_physical_properties for help entering or editing information about the physical properties of this gene product.

Name
Sequence	at EcoCyc MSRVAKAPVV VPAGVDVKIN GQVITIKGKN GELTRTLNDA VEVKHADNTL TFGPRDGYAD GWAQAGTARA LLNSMVIGVT EGFTKKLQLV GVGYRAAVKG NVINLSLGFS HPVDHQLPAG ITAECPTQTE IVLKGADKQV IGQVAADLRA YRRPEPYKGK GVRYADEVVR TKEAKKK
Length	177
Mol. Wt	18.902 kDa
pI	10.1 (calculated)
Extinction coefficient	12,950 - 13,075 (calc based on 5 Y, 1 W, and 1 C residues)
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Domains/Motifs/Modification Sites

See Help:Product_domains_motifs for help entering or editing information in this section of EcoliWiki.

Type	Residues	Description	Notes	References
Initiator Methionine	1	Removed	UniProt:P0AG55
Domain	11..82	PF00347 Ribosomal protein L6		PMID:19920124
Domain	90..165	PF00347 Ribosomal protein L6		PMID:19920124
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<motif_map/>

Structure
See Help:Product_structure for help entering or editing information in this section of EcoliWiki.

Structures

<beststructure> gene=rplF taxon=562,83333 </beststructure>

Models

View models at:

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</protect>

Structure figures

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Notes

Gene Product Resources

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See Help:Product_resources for help with entering or editing information in this section of EcoliWiki.

Resource type	Source	Notes/Reference
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Notes

Accessions in Other Databases

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
NCBI (Protein) (EcoliWiki Page)	GI:16131184	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947803	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010827	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AG55	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10869	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10869	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947803	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000860	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0862	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Expression

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Overview

This is a placeholder for a summary statement on how expression of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Cellular Levels

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See Help:Cellular levels

Molecule	Organism or Strain	Value	Units	Experimental Conditions	Assay used	Reference(s)
Protein	E. coli K-12 MC4100	1.86E+04	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI	PMID:18304323
Protein	E. coli K-12 MG1655	117546	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	16781	molecules/cell/generation	Medium: MOPS Minimal Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
Protein	E. coli K-12 MG1655	71798	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	PMID: 24766808
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Notes

Transcription and Transcriptional Regulation

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See Help:Expression_transcription for help entering or editing information in this section of EcoliWiki.

Transcription unit(s)
rplNXE-rpsNH-rplFR-rpsE-rpmD-rplO-secY-rpmJ
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Figure courtesy of RegulonDB

</protect>

Notes

This is a placeholder for a summary statement about how transcription of this gene is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Translation and Regulation of Translation

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<protect><gbrowseImage> name=NC_000913:3444142..3444182 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

</protect>

Notes

This is a placeholder for a summary statement about how translation of this gene product is regulated. You can help EcoliWiki by becoming a user and writing/editing this statement.

Turnover and Regulation of Turnover

</protect>

Notes

This is a placeholder for a summary statement about turnover of this gene product. You can help EcoliWiki by becoming a user and writing/editing this statement.

Experimental

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<protect> Mutations Affecting Expression See Help:Expression_mutations for help entering or editing information in this section of EcoliWiki.

Allele Name	Mutation	Phenotype	Reference
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Expression Studies See Help:Expression_studies for help entering or editing information in this section of EcoliWiki.

Type	Reference	Notes
microarray	GEO Profiles:b3305 (EcoliWiki Page)	NCBI GEO profiles for rplF
microarray	GenExpDB:b3305 (EcoliWiki Page)	Summary of data for rplF from multiple microarray studies
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Expression Resources See Help:Expression_resources for help entering or editing information in this section of EcoliWiki.

Resource Name	Resource Type	Description	Source	Notes
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Notes

Accessions Related to rplF Expression

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
EcoCyc	EcoCyc:EG10869	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0862	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3305
EcoGene	EcoGene:EG10869	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000860	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010827	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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Evolution

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Homologs in Other Organisms

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See Help:Evolution_homologs for help entering or editing information in this section of EcoliWiki.

Organism	Homologs (Statistics)	Comments
Arabidopsis thaliana	AT1G05190 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0201614 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YHR147C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC12G128 (score: 1.000; bootstrap: 96%)	From Inparanoid:20070104
Shigella flexneri	RPLF	From SHIGELLACYC
E. coli O157	RPLF	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

Families

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See Help:Gene_accessions for help with entering information into the Gene Accessions table.

Database	Accession	Notes
Pfam (EcoliWiki Page)	PF00347 Ribosomal protein L6
Pfam (EcoliWiki Page)	PF00347 Ribosomal protein L6
Panther (EcoliWiki Page)	PTHR11655:SF6
Superfamily (EcoliWiki Page)	SUPERFAMILY:56053
Superfamily (EcoliWiki Page)	SUPERFAMILY:56053
EcoCyc	EcoCyc:EG10869	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10869	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000860	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0862	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010827	Escherichia coli str. K-12 substr. MG1655
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Notes

Links

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Name	URL	Comments
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References

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See Help:References for how to manage references in EcoliWiki.

↑ ^1.0 ^1.1 ^1.2 ^1.3 ^1.4 ^1.5 ^1.6 ^1.7 Riley, M. et al. (2006) Nucleic Acids Res 34:1-6 (corrected supplemental data from B. Wanner)
↑ ^2.0 ^2.1 ^2.2 ^2.3 ^2.4 ^2.5 ^2.6 ^2.7 ^2.8 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 ^3.5 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Davies, C et al. (1998) Ribosomal proteins S5 and L6: high-resolution crystal structures and roles in protein synthesis and antibiotic resistance. J. Mol. Biol. 279 873-88 PubMed
↑ ^6.0 ^6.1 CGSC: The Coli Genetics Stock Center
↑ ^7.0 ^7.1 The Tn10 insertion sites determined by Nichols et al. 1998 (PMID:9829956) were reannotated by alignment with E. coli K-12 genome sequence (GenBank accession NC_000913). P1 contransduction frequencies were calculated using the formula of Wu (PMID:5338813).

rplF:On One Page

Quickview

Notes

Gene

Nomenclature

Notes

Location(s) and DNA Sequence

Notes

Sequence Features

Notes

Alleles and Phenotypes

Notes

Genetic Interactions

Notes

Genetic Resources

Notes

Accessions in Other Databases

Notes

Links

Product(s)

Nomenclature

Notes

Function

Notes

Localization

Notes

Structure and Physical Properties

Structure figures

Notes

Gene Product Resources

Notes

Accessions in Other Databases

Notes

Links

Expression

Overview

Cellular Levels

Notes

Transcription and Transcriptional Regulation

Notes

Translation and Regulation of Translation

Notes

Turnover and Regulation of Turnover

Notes

Experimental

Notes

Accessions Related to rplF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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