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Gene |

Product(s) |

Expression|

Evolution |

References |

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Standard Name	ybjX
Gene Synonym(s)	ECK0868, b0877, JW0861^[1], JW0861
Product Desc.	conserved protein^[2]^[3] Function unknown, homologous to somA (S.t.) and virK (S.f.)^[4]
Product Synonyms(s)	conserved protein^[1], B0877^[2]^[1], YbjX^[2]^[1] , ECK0868, JW0861, b0877
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ybjX^[2]
Regulation/Activity
Quick Links
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See Help:Quickview for help with entering information in the Quickview table.

Notes

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The ybjX homolog somA is an msbB (lpxM) suppressor mutation in Salmonella.^[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	ybjX
Mnemonic	Systematic nomenclature
Synonyms	ECK0868, b0877, JW0861^[1], JW0861
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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	19.77 minutes	MG1655: 918343..917351 <gbrowseImage> name=NC_000913:917351..918343 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 935826..934834 <gbrowseImage> name=NC_012967:934834..935826 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 820319..821311 <gbrowseImage> name=NC_012759:820319..821311 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 919542..918550 <gbrowseImage> name=NC_007779:918550..919542 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 972271..971279 <gbrowseImage> name=NC_010473:971279..972271 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
ΔybjX (Keio:JW0861)	deletion	deletion			PMID:16738554	Shigen CGSC8893^[5]
ΔybjX::kan	deletion		Biolog:respiration	unable to respire Acetate	PMID:16095938
ΔybjX778::kan					PMID:16738554	CGSC:103894
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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
JW0861	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGTGAAATCGACGCCATGTAT Primer 2:CCACCGCGAAACATCGTGGCCAT
1E5	Kohara Phage	Genobase	PMID:3038334
1H1	Kohara Phage	Genobase	PMID:3038334
zbh-29::Tn10	Linked marker	CAG18493 = CGSC7353^[5]	est. P1 cotransduction: % ^[6] Synonyms:zbi-29::Tn10
zca-1230::Tn10	Linked marker	CAG18478 = CGSC7356^[5]	est. P1 cotransduction: 32% ^[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:G6460	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13693	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003060	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946025	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3457	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002982	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	YbjX
Synonyms	conserved protein^[1], B0877^[2]^[1], YbjX^[2]^[1] , ECK0868, JW0861, b0877
Product description	conserved protein^[2]^[3] Function unknown, homologous to somA (S.t.) and virK (S.f.)^[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:0006974	response to DNA damage stimulus	PMID:11967071^[7]	IEP: Inferred from Expression Pattern		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	lpdA	PMID:15690043^[8]	Experiment(s):EBI-879208
Protein	pssA	PMID:15690043^[8]	Experiment(s):EBI-879208
Protein	rplA	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rplB	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rplC	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rplD	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rplE	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rplF	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rplM	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rplV	PMID:15690043^[8]	Experiment(s):EBI-879208
Protein	rpoC	PMID:15690043^[8]	Experiment(s):EBI-879208
Protein	rpsA	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rpsB	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rpsC	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rpsD	PMID:15690043^[8]	Experiment(s):EBI-879208
Protein	rpsG	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	srmB	PMID:15690043^[8]	Experiment(s):EBI-879208
Protein	tufA	PMID:15690043^[8]	Experiment(s):EBI-879208, EBI-882921
Protein	rnr	PMID:15690043^[8]	Experiment(s):EBI-879208
Protein	rluB	PMID:15690043^[8]	Experiment(s):EBI-879208
Protein	rplX	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rpmB	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rpmC	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rpmG	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rpsE	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rpsF	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rpsM	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rpsS	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rpsT	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	aceF	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	dnaJ	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	hupA	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	hupB	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rplI	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rplJ	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rplL	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rplO	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rplQ	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rplS	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rplT	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	rplU	PMID:15690043^[8]	Experiment(s):EBI-882921
Protein	perM	PMID:16606699^[9]	Experiment(s):EBI-1138231
Protein	yciH	PMID:16606699^[9]	Experiment(s):EBI-1138231
Protein	rplB	PMID:16606699^[9]	Experiment(s):EBI-1138231
Protein	appY	PMID:16606699^[9]	Experiment(s):EBI-1138231
Protein	groL	PMID:16606699^[9]	Experiment(s):EBI-1138231
Protein	mutH	PMID:16606699^[9]	Experiment(s):EBI-1138231
Protein	rpmC	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rpmG	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rpmB	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rpsA	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):21.224236
Protein	rplJ	PMID:19402753^[10]	LCMS(ID Probability):99.4 MALDI(Z-score):3.385515
Protein	rplT	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rplO	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rplE	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):27.323521
Protein	rfaD	PMID:19402753^[10]	MALDI(Z-score):38.502110
Protein	rplU	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	tufB	PMID:19402753^[10]	MALDI(Z-score):20.676555
Protein	rplI	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rplF	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):29.180248
Protein	rplQ	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rpsF	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	hupB	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rplS	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):2.654204
Protein	rplM	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):32.496120
Protein	hupA	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rpsD	PMID:19402753^[10]	LCMS(ID Probability):97.9 MALDI(Z-score):34.058088
Protein	rpsM	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rplX	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rpsC	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):26.378458
Protein	rplA	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):23.679102
Protein	rplB	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):37.287562
Protein	srmB	PMID:19402753^[10]	MALDI(Z-score):24.880466
Protein	dnaJ	PMID:19402753^[10]	LCMS(ID Probability):99.6
Protein	rplD	PMID:19402753^[10]	LCMS(ID Probability):99.6 MALDI(Z-score):18.911757
Protein	yfiF	PMID:19402753^[10]	LCMS(ID Probability):97.8 MALDI(Z-score):7.664643
Protein	rnr	PMID:19402753^[10]	MALDI(Z-score):26.041938
Protein	rplL	PMID:19402753^[10]	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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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 MVKSTPCITI DFMNMSQLTE RTFTPSESLS SLSLFLSLAR GQCRPGKFWH RRSFRQKFLL RSLIMPRLSV EWMNELSHWP NLNVLLTRQP RLPVRLHRPY LAANLSRKQL LEALRYHYAL LRECMSAEEF SLYLNTPGLQ LAKLEGKNGE QFTLELTMMI SMDKEGDSTI LFRNSEGIPL AEITFTLCEY QGKRTMFIGG LQGAKWEIPH QEIQNATKAC HGLFPKRLVM EAACLFAQRL QVEQIIAVSN ETHIYRSLRY RDKEGKIHAD YNAFWESVGG VCDAERHYRL PAQIARKEIA EIASKKRAEY RRRYEMLDAI QPQMATMFRG
Length	330
Mol. Wt	38.358 kDa
pI	9.7 (calculated)
Extinction coefficient	43,890 - 44,765 (calc based on 11 Y, 5 W, and 7 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	40..328	PF04393 Protein of unknown function (DUF535)		PMID:19920124^[11]
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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=ybjX 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:16128845	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946025	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002982	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P75829	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6460	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13693	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946025	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003060	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3457	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	9.267+/-0.083	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.106854839	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	2797	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	507	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	2424	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)
ybjX
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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_000913:918323..918363 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:b0877 (EcoliWiki Page)	NCBI GEO profiles for ybjX
microarray	GenExpDB:b0877 (EcoliWiki Page)	Summary of data for ybjX 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 ybjX Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6460	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3457	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0877
EcoGene	EcoGene:EG13693	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003060	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002982	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
Shigella flexneri	YBJX	From SHIGELLACYC
E. coli O157	YBJX	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)	PF04393 Protein of unknown function (DUF535)
EcoCyc	EcoCyc:G6460	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13693	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120003060	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3457	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0002982	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 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.
↑ ^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).
↑ Khil, PP & Camerini-Otero, RD (2002) Over 1000 genes are involved in the DNA damage response of Escherichia coli. Mol. Microbiol. 44 89-105 PubMed
↑ ^8.00 ^8.01 ^8.02 ^8.03 ^8.04 ^8.05 ^8.06 ^8.07 ^8.08 ^8.09 ^8.10 ^8.11 ^8.12 ^8.13 ^8.14 ^8.15 ^8.16 ^8.17 ^8.18 ^8.19 ^8.20 ^8.21 ^8.22 ^8.23 ^8.24 ^8.25 ^8.26 ^8.27 ^8.28 ^8.29 ^8.30 ^8.31 ^8.32 ^8.33 ^8.34 ^8.35 ^8.36 ^8.37 ^8.38 ^8.39 ^8.40 Butland, G et al. (2005) Interaction network containing conserved and essential protein complexes in Escherichia coli. Nature 433 531-7 PubMed
↑ ^9.0 ^9.1 ^9.2 ^9.3 ^9.4 ^9.5 Arifuzzaman, M et al. (2006) Large-scale identification of protein-protein interaction of Escherichia coli K-12. Genome Res. 16 686-91 PubMed
↑ ^10.00 ^10.01 ^10.02 ^10.03 ^10.04 ^10.05 ^10.06 ^10.07 ^10.08 ^10.09 ^10.10 ^10.11 ^10.12 ^10.13 ^10.14 ^10.15 ^10.16 ^10.17 ^10.18 ^10.19 ^10.20 ^10.21 ^10.22 ^10.23 ^10.24 ^10.25 ^10.26 ^10.27 ^10.28 ^10.29 ^10.30 Hu, P et al. (2009) Global functional atlas of Escherichia coli encompassing previously uncharacterized proteins. PLoS Biol. 7 e96 PubMed
↑ Finn, RD et al. (2010) The Pfam protein families database. Nucleic Acids Res. 38 D211-22 PubMed

ybjX: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 ybjX Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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