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Standard Name	rimP
Gene Synonym(s)	ECK3159, b3170, JW5533, yhbC^[1], JW5533, yhbC
Product Desc.	conserved protein^[2]^[3]
Product Synonyms(s)	conserved protein^[1], B3170^[2]^[1], YhbC^[2]^[1] , ECK3159, JW5533, yhbC, b3170
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): rimP-nusA-infB^[2], metY-rimP-nusA-infB-rbfA-truB-rpsO-pnp^[2], metY-rimP-nusA-infB^[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	rimP
Mnemonic	Ribosomal modification
Synonyms	ECK3159, b3170, JW5533, yhbC^[1], JW5533, yhbC
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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	71.46 minutes	MG1655: 3316028..3315576 <gbrowseImage> name=NC_000913:3315576..3316028 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 3202724..3203182 <gbrowseImage> name=NC_012759:3202724..3203182 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 3317861..3317409 <gbrowseImage> name=NC_007779:3317409..3317861 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 3413773..3413321 <gbrowseImage> name=NC_010473:3413321..3413773 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)	Reference	Availability
ΔyhbC (Keio:JW5533)	deletion	deletion	PMID:16738554	Shigen CGSC11448^[4]
ΔyhbC780::kan			PMID:16738554	CGSC:105096
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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
JW5533	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTCCACATTAGAGCAAAAATT Primer 2:CCAAAGTGGGGAACCAGGTTCGC
E4G11S	Kohara Phage	Genobase	PMID:3038334
18H7	Kohara Phage	Genobase	PMID:3038334
aer-3075::Tn10	Linked marker	CAG12152 = CGSC7438^[4]	est. P1 cotransduction: % ^[5] Synonyms:zgh-3075::Tn10, zgj-3075::Tn10
sfsB203::Tn10	Linked marker	CAG12072 = CGSC7440^[4]	est. P1 cotransduction: 57% ^[5] Synonyms:zgj-203::Tn10, zha-203::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
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3170
ECOL199310CYC (EcoliWiki Page)	ECOL199310CYC:C3927
ECOO157CYC (EcoliWiki Page)	ECOO157CYC:YHBC
EcoCyc (EcoliWiki Page)	ECOCYC:EG11179	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:947680	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	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	rimP
Synonyms	conserved protein^[1], B3170^[2]^[1], YhbC^[2]^[1] , ECK3159, JW5533, yhbC, b3170
Product description	conserved protein^[2]^[3]
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:0005737	cytoplasm	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_01077	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GOA:spkw SP_KW:GO_REF:0000004	IEA: Inferred from Electronic Annotation	SP_KW:KW-0963	C	Seeded from EcoCyc (v14.0)	complete
	GO:0005737	cytoplasm	GO_REF:0000023	IEA: Inferred from Electronic Annotation	SP_SL:SL-0086	C	Seeded from EcoCyc (v14.0)	complete
	GO:0042274	ribosomal small subunit biogenesis	PMID:19150615	IMP: Inferred from Mutant Phenotype		P	Increased levels of pre-16S rRNA in the rimP(del) mutant compared to wild-type cells (Fig. 5).	complete
	GO:0006412	translation	PMID:19150615	IMP: Inferred from Mutant Phenotype		P	Fewer polysomes in rimP(del) mutant than in parental strain.	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	References	Evidence
Protein	rpsE	PMID:15690043	Experiment(s):EBI-881698
Protein	rpsG	PMID:15690043	Experiment(s):EBI-881698
Protein	yihI	PMID:15690043	Experiment(s):EBI-882361
Protein	yihI	PMID:19402753	LCMS(ID Probability):99.6
Protein	rpsC	PMID:19402753	LCMS(ID Probability):99.0 MALDI(Z-score):8.524008
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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 MGLSTLEQKL TEMITAPVEA LGFELVGIEF IRGRTSTLRI YIDSEDGINV DDCADVSHQV SAVLDVEDPI TVAYNLEVSS PGLDRPLFTA EHYARFVGEE VTLVLRMAVQ NRRKWQGVIK AVDGEMITVT VEGKDEVFAL SNIQKANLVP HF
Length	152
Mol. Wt	16.82 kDa
pI	4.5 (calculated)
Extinction coefficient	9,970 - 10,095 (calc based on 3 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
Domain	13..148	PF02576 Uncharacterised BCR, YhbC family COG0779		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=yhbC 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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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:226524751	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:947680	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8A8	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:947680	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	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	Notes	Reference(s)
Protein	Ecoli K-12	44.951+/-0.259	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.184734513	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by RNA_Seq	PMID:20671182
Protein	E. coli K-12 MG1655	6151	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	1220	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	3040	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)
yhbC-nusA-infB
metY-yhbC-nusA-infB-rbfA-truB-rpsO-pnp
metY-yhbC-nusA-infB
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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_000913:3316008..3316048 source=MG1655 flip=1 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:b3170 (EcoliWiki Page)	NCBI GEO profiles for yhbC
microarray	GenExpDB:b3170 (EcoliWiki Page)	Summary of data for yhbC 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 (3315585..3315904) fused to gfpmut2.	OpenBioSystems	GFP fusion described in Zaslaver, et al. Plate:109-AZ09; Well:B9^[6]
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Notes

Accessions Related to rimP Expression

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

Database	Accession	Notes
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b3170
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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
Xenopus tropicalis	ENSXETP00000040923 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YHBC	From SHIGELLACYC
E. coli O157	YHBC	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)	PF02576 Uncharacterised BCR, YhbC family COG0779
Superfamily (EcoliWiki Page)	SUPERFAMILY:74942
Superfamily (EcoliWiki Page)	SUPERFAMILY:75420
PFAM (EcoliWiki Page)	PFAM:PF02576
EcoCyc	EcoCyc:	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:	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 EcoCyc (release 11.1; 2007) Keseler, IM et al. (2005) Nucleic Acids Res. 33(Database issue):D334-7
↑ ^4.0 ^4.1 ^4.2 CGSC: The Coli Genetics Stock Center
↑ ^5.0 ^5.1 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).
↑ Zaslaver, A et al. (2006) A comprehensive library of fluorescent transcriptional reporters for Escherichia coli. Nat. Methods 3 623-8 PubMed

rimP: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 rimP Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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