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On One Page

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Expression|

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Standard Name	rimI
Gene Synonym(s)	ECK4364, b4373, JW4335^[1], JW4335
Product Desc.	EG10850- Modification of 30S ribosomal subunit protein S18; acetylation of N-terminal alanine^[2]
Product Synonyms(s)	acetylase for 30S ribosomal subunit protein S18 ^[1], B4373 ^[3]^[1], RimI ^[3]^[1] , ECK4364, JW4335, b4373
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): holD^[3]
Regulation/Activity
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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	rimI
Mnemonic	Ribosomal modification
Synonyms	ECK4364, b4373, JW4335^[1], JW4335
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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	99.28 minutes	MG1655: 4606208..4606654 <gbrowseImage> name=NC_000913:4606208..4606654 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4597419..4597865 <gbrowseImage> name=NC_012967:4597419..4597865 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4544692..4545138 <gbrowseImage> name=NC_012759:4544692..4545138 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4612865..4613311 <gbrowseImage> name=NC_007779:4612865..4613311 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4652670..4653116 <gbrowseImage> name=NC_010473:4652670..4653116 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
ΔrimI (Keio:JW4335)	deletion	deletion	PMID:16738554	Shigen CGSC11092^[4]
ΔrimI768::kan			PMID:16738554	CGSC:102718
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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
JW4335	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAACACGATTTCTTCCCTCGA Primer 2:CCCATACTGATTGGCAACGCCAT
5C1	Kohara Phage	Genobase	PMID:3038334
mdoB202::Tn10	Linked marker	CAG18430 = CGSC7488^[4]	est. P1 cotransduction: 64% ^[5] Synonyms:zjj-202::Tn10, zji-202::Tn10
thrA34::Tn10	Linked marker	CAG18442 = CGSC7320^[4]	est. P1 cotransduction: 26% ^[5] Synonyms:thr-34::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:EG10850	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10850	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000841	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948894	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0843	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014342	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	RimI
Synonyms	acetylase for 30S ribosomal subunit protein S18 ^[1], B4373 ^[3]^[1], RimI ^[3]^[1] , ECK4364, JW4335, b4373
Product description	EG10850- Modification of 30S ribosomal subunit protein S18; acetylation of N-terminal alanine^[2]
EC number (for enzymes)	2.3.1.128^[1]
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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:0006464	protein modification process				P	Seeded from Riley et al 2006 ^[1].	Missing: evidence, reference
	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:0017189	N-terminal peptidyl-alanine acetylation	PMID:6991870	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0006474	N-terminal protein amino acid acetylation	PMID:6991870	IMP: Inferred from Mutant Phenotype		P		complete
	GO:0008080	N-acetyltransferase activity	PMID:6991870	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0008999	ribosomal-protein-alanine N-acetyltransferase activity	PMID:6991870	IMP: Inferred from Mutant Phenotype		F		complete
	GO:0006464	protein modification process	PMID:6991870	IMP: Inferred from Mutant Phenotype		P		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	tig	PMID:19402753	MALDI(Z-score):35.541182
Protein	glpK	PMID:19402753	MALDI(Z-score):19.841268
Protein	pgk	PMID:19402753	MALDI(Z-score):30.718705
Protein	rfaD	PMID:19402753	MALDI(Z-score):43.986553
Protein	rpoA	PMID:19402753	MALDI(Z-score):23.948276
Protein	yfiD	PMID:19402753	MALDI(Z-score):28.270154
Protein	phoA	PMID:19402753	MALDI(Z-score):18.292817
Protein	adhE	PMID:19402753	MALDI(Z-score):23.839585
Protein	clpB	PMID:19402753	MALDI(Z-score):18.497373
Protein	pstS	PMID:19402753	MALDI(Z-score):35.771269
Protein	fusA	PMID:19402753	MALDI(Z-score):26.949439
Protein	gapA	PMID:19402753	MALDI(Z-score):34.419816
Protein	tufB	PMID:19402753	MALDI(Z-score):30.158596
Protein	tsf	PMID:19402753	MALDI(Z-score):23.379486
Protein	lysU	PMID:19402753	MALDI(Z-score):18.195740
Protein	udp	PMID:19402753	MALDI(Z-score):27.588620
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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 MNTISSLETT DLPAAYHIEQ RAHAFPWSEK TFASNQGERY LNFQLTQNGK MAAFAITQVV LDEATLFNIA VDPDYQRQGL GRALLEHLID ELEKRGVATL WLEVRASNAA AIALYESLGF NEATIRRNYY PTTDGREDAI IMALPISM
Length	148
Mol. Wt	16.609 kDa
pI	4.7 (calculated)
Extinction coefficient	19,940 (calc based on 6 Y, 2 W, and 0 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	45..121	PF00583 Acetyltransferase (GNAT) family		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=rimI taxon=562,83333 </beststructure>

Models

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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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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:16132191	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948894	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014342	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A944	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG10850	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10850	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948894	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000841	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0843	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	625	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	156	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	175	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)
holD
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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_000913:4606188..4606228 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:b4373 (EcoliWiki Page)	NCBI GEO profiles for rimI
microarray	GenExpDB:b4373 (EcoliWiki Page)	Summary of data for rimI 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 rimI Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG10850	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0843	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4373
EcoGene	EcoGene:EG10850	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000841	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014342	Escherichia coli str. K-12 substr. MG1655
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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
Drosophila melanogaster	FBgn0052319 (score: 1.000; bootstrap: 100%) FBgn0024362 (score: 0.285)	From Inparanoid:20070104
Drosophila pseudoobscura	GA16829-PA (score: 1.000; bootstrap: 100%) GA10986-PA (score: 0.429)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000036637 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	RIMI	From SHIGELLACYC
E. coli O157	RIMI	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)	PF00583 Acetyltransferase (GNAT) family
Panther (EcoliWiki Page)	PTHR23091:SF1
Superfamily (EcoliWiki Page)	SUPERFAMILY:55729
EcoCyc	EcoCyc:EG10850	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG10850	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120000841	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB0843	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0014342	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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ ^3.0 ^3.1 ^3.2 ^3.3 ^3.4 EcoCyc (release 10.6; 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).

rimI:On One Page

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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 rimI Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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