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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

References |

Quickview

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Standard Name	rpsM
Gene Synonym(s)	ECK3285, b3298, JW3260^[1], JW3260
Product Desc.	30S ribosomal subunit protein S13^[2]^[3]; Component of 30S ribosomal subunit^[2]^[3]; ribosome^[2]^[3] 30S ribosomal subunit protein S13^[4]
Product Synonyms(s)	30S ribosomal subunit protein S13^[1], B3298^[2]^[1], RpsM^[2]^[1] , ECK3285, JW3260, b3298
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rpsMKD-rpoA-rplQ^[2]
Regulation/Activity
Quick Links
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Notes

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rpsM can be deleted, but null mutants grow slowly and express kanamycin resistance weakly (Bubunenko, 2007), which may explain why a deletion was not isolated by Baba (2006), leading to its misclassification as an essential gene.^[4]

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	rpsM
Mnemonic	Ribosomal protein, small
Synonyms	ECK3285, b3298, JW3260^[1], JW3260
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Notes

Location(s) and DNA Sequence

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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	74.15 minutes	MG1655: 3440493..3440137 <gbrowseImage> name=NC_000913:3440137..3440493 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 3370376..3370020 <gbrowseImage> name=NC_012967:3370020..3370376 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 3327294..3327650 <gbrowseImage> name=NC_012759:3327294..3327650 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4197945..4198301 <gbrowseImage> name=NC_007779:4197945..4198301 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3538238..3537882 <gbrowseImage> name=NC_010473:3537882..3538238 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	3440140	Edman degradation	PMID:330375
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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	AA change(s)	Phenotype: Type	Phenotype: Description	Reference	Comments
rpsM					Deletion
rpsM					Deletion
rpsMN105H	N105H		(in PW095; partially suppresses a rimM deletion)		Strain variation; seeded from UniProt:P0A7S9
rpsMN105K	N105K		(in PW097; partially suppresses a rimM deletion)		Strain variation; seeded from UniProt:P0A7S9
rpsM					Deletion
rpsM					Deletion
Ksg^d rpsM MV34		Antibiotic Dependence	Kasugamycin Dependence	PMID:363701	See figure 2 for portions of two-dimensional gel electropherogram of 70s ribosome protien.
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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
JW3260	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCCCGTATAGCAGGCATTAA Primer 2:CCTTTCTTGATCGGTTTGCGCGG
E1H9	Kohara Phage	Genobase	PMID:3038334
smg-3082::Tn10	Linked marker	CAG12071 = CGSC7444^[5]	est. P1 cotransduction: 67% ^[6] Synonyms:zhb-3082::Tn10, zhd-3082::Tn10
zhf-3084::Tn10	Linked marker	CAG18456 = CGSC7576^[5]	est. P1 cotransduction: 3% ^[6] 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:EG10912	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10912	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000903	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947791	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0905	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010809	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	RpsM
Synonyms	30S ribosomal subunit protein S13^[1], B3298^[2]^[1], RpsM^[2]^[1] , ECK3285, JW3260, b3298
Product description	30S ribosomal subunit protein S13^[2]^[3]; Component of 30S ribosomal subunit^[2]^[3]; ribosome^[2]^[3] 30S ribosomal subunit protein S13^[4]
EC number (for enzymes)
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Notes

Function

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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:0000049	tRNA binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0820	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003676	nucleic acid binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR010979	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001892	F	Seeded from EcoCyc (v14.0)	complete
	GO:0022627	cytosolic small ribosomal subunit	PMID:4587209^[7]	IDA: Inferred from Direct Assay		C		complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018269	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003723	RNA binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019980	F	Seeded from EcoCyc (v14.0)	complete
	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:IPR001892	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003735	structural constituent of ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018269	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003735	structural constituent of ribosome	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019980	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01315	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR001892	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR018269	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR019980	P	Seeded from EcoCyc (v14.0)	complete
	GO:0019843	rRNA binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01315	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
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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 30S ribosomal subunit	could be indirect
Protein	rpsG		PMID:16606699^[8]	Experiment(s):EBI-1145459, EBI-1145603
Protein	ycgE		PMID:16606699^[8]	Experiment(s):EBI-1145459
Protein	rplB		PMID:16606699^[8]	Experiment(s):EBI-1145459
Protein	rpsC		PMID:16606699^[8]	Experiment(s):EBI-1145459
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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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 MARIAGINIP DHKHAVIALT SIYGVGKTRS KAILAAAGIA EDVKISELSE GQIDTLRDEV AKFVVEGDLR REISMSIKRL MDLGCYRGLR HRRGLPVRGQ RTKTNARTRK GPRKPIKK
Length	118
Mol. Wt	13.099 kDa
pI	11.2 (calculated)
Extinction coefficient	2,980 - 3,105 (calc based on 2 Y, 0 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:P0A7S9
Domain	3..108	PF00416 Ribosomal protein S13/S18		PMID:19920124^[9]
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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=rpsM taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

Notes

Gene Product Resources

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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:16131177	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947791	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010809	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A7S9	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10912	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10912	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947791	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000903	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0905	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	3.12E+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	118618	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	19239	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	70243	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)
rpsMKD-rpoA-rplQ
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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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<gbrowseImage> name=NC_000913:3440473..3440513 source=MG1655 flip=1 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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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:b3298 (EcoliWiki Page)	NCBI GEO profiles for rpsM
microarray	GenExpDB:b3298 (EcoliWiki Page)	Summary of data for rpsM 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
	GFP Fusion	Intergenic region (3440017..3440284) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ19; Well:C8^[10]
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Notes

Accessions Related to rpsM Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10912	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0905	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3298
EcoGene	EcoGene:EG10912	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000903	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010809	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
Apis mellifera	ENSAPMP00000020142 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G14320 (score: 1.000; bootstrap: 99%) AT1G77750 (score: 0.083)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000003431 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-020419-20 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-762 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0010411 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA21399-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000211372 (score: 1.000; bootstrap: 100%) ENSP00000354469 (score: 0.980) ENSP00000352029 (score: 0.941) ENSP00000328456 (score: 0.736)	From Inparanoid:20070104
Mus musculus	MGI:98146 (score: 1.000; bootstrap: 100%) MGI:3644667 (score: 0.837) MGI:3645266 (score: 0.821) MGI:3644447 (score: 0.813) MGI:3644672 (score: 0.802) MGI:3647485 (score: 0.679)	From Inparanoid:20070104
Oryza gramene	Q75IA5 (score: 1.000; bootstrap: 92%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000030810 (score: 1.000; bootstrap: 100%) ENSPTRP00000026184 (score: 0.953) ENSPTRP00000039838 (score: 0.937) ENSPTRP00000011287 (score: 0.740)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000046090 (score: 1.000; bootstrap: 100%) ENSRNOP00000047371 (score: 0.976) ENSRNOP00000030371 (score: 0.976) ENSRNOP00000049793 (score: 0.925) ENSRNOP00000040056 (score: 0.902) ENSRNOP00000044731 (score: 0.654) ENSRNOP00000040282 (score: 0.626)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNL081C (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC17957 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000153006 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000043401 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	RPSM	From SHIGELLACYC
E. coli O157	RPSM	From ECOO157CYC
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Notes

Families

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

Database	Accession	Notes
Superfamily (EcoliWiki Page)	SUPERFAMILY:46946
Panther (EcoliWiki Page)	PTHR10871:SF1
Pfam (EcoliWiki Page)	PF00416 Ribosomal protein S13/S18
EcoCyc	EcoCyc:EG10912	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10912	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000903	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0905	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0010809	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)
↑ ^2.00 ^2.01 ^2.02 ^2.03 ^2.04 ^2.05 ^2.06 ^2.07 ^2.08 ^2.09 ^2.10 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 ^4.2 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^5.0 ^5.1 CGSC: The Coli Genetics Stock Center
↑ ^6.0 ^6.1 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).
↑ Wittmann-Liebold, B (1973) Studies on the primary structure of 20 proteins from Escherichia coli ribosomes by means of an improved protein sequenator. FEBS Lett. 36 247-9 PubMed
↑ ^8.0 ^8.1 ^8.2 ^8.3 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rpsM:On One Page

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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 rpsM Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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