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Product(s) |

Expression|

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Standard Name	rimK
Gene Synonym(s)	ECK0843, b0852, JW0836, nek^[1], nek
Product Desc.	ribosomal protein S6 modification protein^[2]^[3] Modification of RpsF by addition of glutamic acid residues^[4]
Product Synonyms(s)	ribosomal protein S6 modification protein^[1], B0852^[2]^[1], Nek^[2]^[1], RimK^[2]^[1] , ECK0843, JW0836, nek, b0852
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rimK-ybjN^[2], ybjC-nfsA-rimK-ybjN^[2]
Regulation/Activity
Quick Links
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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	rimK
Mnemonic	Ribosomal modification
Synonyms	ECK0843, b0852, JW0836, nek^[1], nek
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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	19.21 minutes	MG1655: 891190..892092 <gbrowseImage> name=NC_000913:891190..892092 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 908674..909576 <gbrowseImage> name=NC_012967:908674..909576 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 794158..795060 <gbrowseImage> name=NC_012759:794158..795060 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 892389..893291 <gbrowseImage> name=NC_007779:892389..893291 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 945118..946020 <gbrowseImage> name=NC_010473:945118..946020 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
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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
ΔrimK (Keio:JW0836)	deletion	deletion			PMID:16738554	Shigen CGSC8873^[5]
nek-728				no gene name nek in CGSC		CGSC:12165
ΔrimK753::kan					PMID:16738554	CGSC:102720
rimK	deletion		Sensitivity to	increases sensitivity to bicyclomycin	PMID:21357484		fig 2
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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
JW0836	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAAATTGCCATATTGTCCCG Primer 2:CCACCACCCGTTTTCAGGCAATA
5F4	Kohara Phage	Genobase	PMID:3038334
zbh-29::Tn10	Linked marker	CAG18493 = CGSC7353^[5]	est. P1 cotransduction: 1% ^[6] Synonyms:zbi-29::Tn10
zca-1230::Tn10	Linked marker	CAG18478 = CGSC7356^[5]	est. P1 cotransduction: 7% ^[6] Synonyms:zbj-1230::Tn10
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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:EG10852	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10852	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000843	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945484	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0845	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002903	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	RimK
Synonyms	ribosomal protein S6 modification protein^[1], B0852^[2]^[1], Nek^[2]^[1], RimK^[2]^[1] , ECK0843, JW0836, nek, b0852
Product description	ribosomal protein S6 modification protein^[2]^[3] Modification of RpsF by addition of glutamic acid residues^[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:0000166	nucleotide binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0547	F	Seeded from EcoCyc (v14.0)	complete
	GO:0000287	magnesium ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0460	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011761	F	Seeded from EcoCyc (v14.0)	complete
	GO:0003824	catalytic activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013816	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01552	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR011761	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR013816	F	Seeded from EcoCyc (v14.0)	complete
	GO:0005524	ATP binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0067	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01552	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006412	translation	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0648	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006464	protein modification process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR004666	P	Seeded from EcoCyc (v14.0)	complete
	GO:0030145	manganese ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0464	F	Seeded from EcoCyc (v14.0)	complete
	GO:0046872	metal ion binding	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0479	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
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Notes

Localization

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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 MKIAILSRDG TLYSCKRLRE AAIQRGHLVE ILDPLSCYMN INPAASSIHY KGRKLPHFDA VIPRIGTAIT FYGTAALRQF EMLGSYPLNE SVAIARARDK LRSMQLLARQ GIDLPVTGIA HSPDDTSDLI DMVGGAPLVV KLVEGTQGIG VVLAETRQAA ESVIDAFRGL NAHILVQEYI KEAQGCDIRC LVVGDEVVAA IERRAKEGDF RSNLHRGGAA SVASITPQER EIAIKAARTM ALDVAGVDIL RANRGPLVME VNASPGLEGI EKTTGIDIAG KMIRWIERHA TTEYCLKTGG
Length	300
Mol. Wt	32.436 kDa
pI	8.3 (calculated)
Extinction coefficient	15,930 - 16,555 (calc based on 7 Y, 1 W, and 5 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
Domain	97..286	PF08443 RimK-like ATP-grasp domain		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=rimK taxon=562,83333 </beststructure>

Models

View models at:

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Structure figures

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Notes

Gene Product Resources

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Resource type	Source	Notes/Reference
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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:16128820	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945484	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002903	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0C0U4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10852	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10852	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945484	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000843	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0845	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 MG1655	101	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	46	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	59	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)
rimK-ybjN
ybjC-nfsA-rimK-ybjN
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Figure courtesy of RegulonDB

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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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<protect><gbrowseImage> name=NC_000913:891170..891210 source=MG1655 type=Gene+DNA_+Protein preset=Nterminus </gbrowseImage> This picture shows the sequence around the N-terminus.

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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

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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:b0852 (EcoliWiki Page)	NCBI GEO profiles for rimK
microarray	GenExpDB:b0852 (EcoliWiki Page)	Summary of data for rimK 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 rimK Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10852	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0845	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0852
EcoGene	EcoGene:EG10852	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000843	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002903	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
Bos taurus	ENSBTAP00000023262 (score: 1.000; bootstrap: 100%) ENSBTAP00000004262 (score: 0.611)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000020456 (score: 1.000; bootstrap: 100%) ENSCAFP00000003727 (score: 0.633)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040912-20 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040912-22 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000023045 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000350136 (score: 1.000; bootstrap: 100%) ENSP00000343675 (score: 0.649) ENSP00000324766 (score: 0.553)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000029852 (score: 1.000; bootstrap: 100%) ENSMMUP00000017241 (score: 0.428)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000022444 (score: 1.000; bootstrap: 100%) ENSMODP00000021607 (score: 0.665)	From Inparanoid:20070104
Mus musculus	MGI:1918325 (score: 1.000; bootstrap: 100%) MGI:3040686 (score: 0.493)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000007924 (score: 1.000; bootstrap: 100%) ENSPTRP00000001047 (score: 0.641) ENSPTRP00000023897 (score: 0.598)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000028923 (score: 1.000; bootstrap: 100%) ENSRNOP00000011586 (score: 0.524)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000140490 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00013753001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000020712 (score: 1.000; bootstrap: 100%) ENSXETP00000029485 (score: 0.555)	From Inparanoid:20070104
Shigella flexneri	RIMK	From SHIGELLACYC
E. coli O157	RIMK	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
Panther (EcoliWiki Page)	PTHR21621:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:56059
Pfam (EcoliWiki Page)	PF08443 RimK-like ATP-grasp domain
EcoCyc	EcoCyc:EG10852	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10852	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000843	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0845	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002903	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 ^1.8 ^1.9 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 ^2.9 EcoCyc (release 10.6; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^3.0 ^3.1 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.
↑ ^5.0 ^5.1 ^5.2 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).

rimK: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 rimK Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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