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Gene |

Product(s) |

Expression|

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Standard Name	rarA
Gene Synonym(s)	ycaJ, ECK0883, b0892, JW0875^[1]^[2], JW0875
Product Desc.	recombination factor^[2]^[3] Involved in processing recombnation intermediates at replication forks, affecting dimer formation; grows poorly when combined with xer or dif mutations; homologous to dnaX and ruvB^[4]
Product Synonyms(s)	recombination protein^[1], B0892^[2]^[1], YcaJ^[2]^[1] , ECK0883, JW0875, ycaJ, b0892
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): lolA^[2]
Regulation/Activity
Quick Links
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Notes

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The paper that designated ycaJ as rarA is Barre et al ^[5]

AFMB Structural Genomics target No. 8 (http://afmb.cnrs-mrs.fr/article171.html)^[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	rarA
Mnemonic	Replication associated recombination
Synonyms	ycaJ, ECK0883, b0892, JW0875^[1]^[2], JW0875
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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	20.2 minutes	MG1655: 937217..938560 <gbrowseImage> name=NC_000913:937217..938560 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
BW2952		NC_012759: 840185..841528 <gbrowseImage> name=NC_012759:840185..841528 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 938416..939759 <gbrowseImage> name=NC_007779:938416..939759 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	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
ΔrarA (Keio:JW0994)	deletion	deletion			PMID:16738554	Shigen CGSC8978^[6]
ΔycaJ::kan	deletion		Biolog:respiration	unable to respire a-D-Glucose-6-phosphate	PMID:16095938
ΔycaJ::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔycaJ::kan	deletion		Biolog:respiration	unable to respire a-Ketobutyrate	PMID:16095938
ΔrarA753::kan					PMID:16738554	CGSC:102592
ΔrarA788::kan					PMID:16738554	CGSC:106300
xerC rarA			Cell Shape	Filamentation- >15% of cells filament	PMID:15065657
dif rarA			Cell Shape	Filamentation- >15% of cells filament	PMID:15065657
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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
JW0994	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCAAACTTTCACTCTCACCTCC Primer 2:CCCAGGGCGGCTTCACGGTGATG
1F10	Kohara Phage	Genobase	PMID:3038334
E6H3	Kohara Phage	Genobase	PMID:3038334
5A12	Kohara Phage	Genobase	PMID:3038334
7B5	Kohara Phage	Genobase	PMID:3038334
zcc-282::Tn10	Linked marker	CAG18466 = CGSC7359^[6]	est. P1 cotransduction: 77% ^[7]
zce-726::Tn10	Linked marker	CAG12078 = CGSC7361^[6]	est. P1 cotransduction: % ^[7]
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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:EG12690	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12690	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002355	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:945505	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2553	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003034	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	YcaJ
Synonyms	recombination protein^[1], B0892^[2]^[1], YcaJ^[2]^[1] , ECK0883, JW0875, ycaJ, b0892
Product description	recombination factor^[2]^[3] Involved in processing recombnation intermediates at replication forks, affecting dimer formation; grows poorly when combined with xer or dif mutations; homologous to dnaX and ruvB^[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:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003593	F	Seeded from EcoCyc (v14.0)	complete
	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:0005524	ATP binding	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003959	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:0017111	nucleoside-triphosphatase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR003593	F	Seeded from EcoCyc (v14.0)	complete
	GO:0030894	replisome	PMID:12864855	IDA: Inferred from Direct Assay		C		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	cadB	PMID:15690043	Experiment(s):EBI-887499
Protein	napH	PMID:15690043	Experiment(s):EBI-887499
Protein	potC	PMID:15690043	Experiment(s):EBI-887499
Protein	rplL	PMID:15690043	Experiment(s):EBI-887499
Protein	yihN	PMID:15690043	Experiment(s):EBI-887499
Protein	cadB	PMID:19402753	LCMS(ID Probability):99.6
Protein	potC	PMID:19402753	LCMS(ID Probability):99.6
Protein	yihN	PMID:19402753	LCMS(ID Probability):99.6
Protein	napH	PMID:19402753	LCMS(ID Probability):99.6
Protein	rplL	PMID:19402753	LCMS(ID Probability):99.6
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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 MSNLSLDFSD NTFQPLAARM RPENLAQYIG QQHLLAAGKP LPRAIEAGHL HSMILWGPPG TGKTTLAEVI ARYANADVER ISAVTSGVKE IREAIERARQ NRNAGRRTIL FVDEVHRFNK SQQDAFLPHI EDGTITFIGA TTENPSFELN SALLSRARVY LLKSLSTEDI EQVLTQAMED KTRGYGGQDI VLPDETRRAI AELVNGDARR ALNTLEMMAD MAEVDDSGKR VLKPELLTEI AGERSARFDN KGDRFYDLIS ALHKSVRGSA PDAALYWYAR IITAGGDPLY VARRCLAIAS EDVGNADPRA MQVAIAAWDC FTRVGPAEGE RAIAQAIVYL ACAPKSNAVY TAFKAALADA RERPDYDVPV HLRNAPTKLM KEMGYGQEYR YAHDEANAYA AGEVYFPPEI AQTRYYFPTN RGLEGKIGEK LAWLAEQDQN SPIKRYR
Length	447
Mol. Wt	49.627 kDa
pI	6.4 (calculated)
Extinction coefficient	50,310 - 50,685 (calc based on 19 Y, 4 W, and 3 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	References
Domain	53..165	PF00004 ATPase family associated with various cellular activities (AAA)	PMID:19920124
Domain	268..436	PF12002 MgsA AAA+ ATPase C terminal	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=rarA 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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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:16128859	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:945505	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003034	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0AAZ4	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG12690	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12690	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:945505	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002355	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2553	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	8.66+/-0.067	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.020848846	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	309	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	95	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	198	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)
lolA
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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_000913:937197..937237 source=MG1655 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

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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:b0892 (EcoliWiki Page)	NCBI GEO profiles for rarA
microarray	GenExpDB:b0892 (EcoliWiki Page)	Summary of data for rarA 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 rarA Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG12690	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2553	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0892
EcoGene	EcoGene:EG12690	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002355	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003034	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
Anopheles gambiae	ENSANGP00000017992 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000011336 (score: 1.000; bootstrap: 98%)	From Inparanoid:20070104
Arabidopsis thaliana	AT1G24290 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000008108 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000013587 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040426-2415 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040425-3362 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0168762 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000020938 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000244490 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000009360 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000010186 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1926153 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000023332 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YNL218W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPAC26H52c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000127060 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00016212001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000020579 (score: 1.000; bootstrap: 99%)	From Inparanoid:20070104
Shigella flexneri	YCAJ	From SHIGELLACYC
E. coli O157	YCAJ	From ECOO157CYC
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Do-It-Yourself Web Tools

Notes

A discussion of RarA's identity to other proteins within E.coli and in other organisms in found in Barre et al. (2001)^[8].

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)	PF00004 ATPase family associated with various cellular activities (AAA)
Superfamily (EcoliWiki Page)	SUPERFAMILY:52540
Panther (EcoliWiki Page)	PTHR13779:SF12
Pfam (EcoliWiki Page)	PF12002 MgsA AAA+ ATPase C terminal
EcoCyc	EcoCyc:EG12690	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG12690	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002355	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB2553	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0003034	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 EcoGene: Rudd, KE (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28:60-4.
↑ Barre, FX et al. (2001) Circles: the replication-recombination-chromosome segregation connection. Proc. Natl. Acad. Sci. U.S.A. 98 8189-95 PubMed
↑ ^6.0 ^6.1 ^6.2 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).
↑ Barre, FX et al. (2001) Circles: the replication-recombination-chromosome segregation connection. Proc. Natl. Acad. Sci. U.S.A. 98 8189-95 PubMed

rarA: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 rarA Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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