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Product(s) |

Expression|

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Standard Name	yjeF
Gene Synonym(s)	ECK4163, b4167, JW4125^[1], JW4125
Product Desc.	predicted carbohydrate kinase^[2]^[3] Putative kinase, ribokinase-like superfamily^[4]
Product Synonyms(s)	predicted carbohydrate kinase^[1], B4167^[2]^[1], YjeF^[2]^[1] , ECK4163, JW4125, b4167
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): yjeFE-amiB-mutL-miaA-hfq-hflXKC^[2], ORF55-ORF17-amiB-mutL-miaA-hfq-hflXKC
Regulation/Activity
Quick Links
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Notes

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Insertions in yjeF indicate this gene is likely to be non-essential. YjeF is homologous to B. subtilis YxkO which belongs to the UPF0031 family. AFMB Structural Genomics target No. 61 (http://afmb.cnrs-mrs.fr/article171.html). otherPDB (B. subtilis): 1KYH.^[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	yjeF
Mnemonic	Systematic nomenclature
Synonyms	ECK4163, b4167, JW4125^[1], JW4125
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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	94.66 minutes	MG1655: 4392089..4393636 <gbrowseImage> name=NC_000913:4392089..4393636 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 4372221..4373768 <gbrowseImage> name=NC_012967:4372221..4373768 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 4330824..4332371 <gbrowseImage> name=NC_012759:4330824..4332371 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 4398746..4400293 <gbrowseImage> name=NC_007779:4398746..4400293 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 4492451..4493998 <gbrowseImage> name=NC_010473:4492451..4493998 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
ΔyjeF (Keio:JW4125)	deletion	deletion			PMID:16738554	Shigen
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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
JW4125	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCACGGACCATACAATGAAGAA Primer 2:CCGGGAGCGGAATTACTCGATTC
3A1	Kohara Phage	Genobase	PMID:3038334
cadB2231::Tn10	Linked marker	CAG18488 = CGSC7479^[5]	est. P1 cotransduction: 24% ^[6] Synonyms:zjd-2231::Tn10
cycA30::Tn10	Linked marker	CAG12073 = CGSC7482^[5]	est. P1 cotransduction: 25% ^[6]
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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:EG11758	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11758	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001694	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:948685	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1708	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013644	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	YjeF
Synonyms	predicted carbohydrate kinase^[1], B4167^[2]^[1], YjeF^[2]^[1] , ECK4163, JW4125, b4167
Product description	predicted carbohydrate kinase^[2]^[3] Putative kinase, ribokinase-like superfamily^[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
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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	aceF	PMID:15690043	Experiment(s):EBI-886481, EBI-892878
Protein	lpdA	PMID:15690043	Experiment(s):EBI-886481, EBI-892878
Protein	mraZ	PMID:15690043	Experiment(s):EBI-886481, EBI-892878
Protein	rhsC	PMID:16606699	Experiment(s):EBI-1147600
Protein	yfhM	PMID:16606699	Experiment(s):EBI-1147600
Protein	mraZ	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):37.274163
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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 MTDHTMKKNP VSIPHTVWYA DDIRRGEREA ADVLGLTLYE LMLRAGEAAF QVCRSAYPDA RHWLVLCGHG NNGGDGYVVA RLAKAVGIEV TLLAQESDKP LPEEAALARE AWLNAGGEIH ASNIVWPESV DLIVDALLGT GLRQAPRESI SQLIDHANSH PAPIVAVDIP SGLLAETGAT PGAVINADHT ITFIALKPGL LTGKARDVTG QLHFDSLGLD SWLAGQETKI QRFSAEQLSH WLKPRRPTSH KGDHGRLVII GGDHGTAGAI RMTGEAALRA GAGLVRVLTR SENIAPLLTA RPELMVHELT MDSLTESLEW ADVVVIGPGL GQQEWGKKAL QKVENFRKPM LWDADALNLL AINPDKRHNR VITPHPGEAA RLLGCSVAEI ESDRLHCAKR LVQRYGGVAV LKGAGTVVAA HPDALGIIDA GNAGMASGGM GDVLSGIIGA LLGQKLSPYD AACAGCVAHG AAADVLAARF GTRGMLATDL FSTLQRIVNP EVTDKNHDES SNSAP
Length	515
Mol. Wt	54.65 kDa
pI	6.4 (calculated)
Extinction coefficient	58,440 - 59,190 (calc based on 6 Y, 9 W, and 6 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	257..496	PF01256 Carbohydrate kinase	PMID:19920124
Domain	34..199	PF03853 YjeF-related protein N-terminus	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=yjeF 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:16131989	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:948685	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013644	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P31806	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11758	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11758	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:948685	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001694	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1708	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	96	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	173	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	77	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)
yjeFE-amiB-mutL-miaA-hfq-hflXKC
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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_000913:4392069..4392109 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:b4167 (EcoliWiki Page)	NCBI GEO profiles for yjeF
microarray	GenExpDB:b4167 (EcoliWiki Page)	Summary of data for yjeF 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 yjeF Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11758	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1708	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b4167
EcoGene	EcoGene:EG11758	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001694	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013644	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	ENSANGP00000025898 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Apis mellifera	ENSAPMP00000031169 (score: 1.000; bootstrap: 85%)	From Inparanoid:20070104
Arabidopsis thaliana	AT5G19150 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000035218 (score: 1.000; bootstrap: 56%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00029031 (score: 1.000; bootstrap: 61%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00011298 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000009128 (score: 1.000; bootstrap: 54%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000006335 (score: 1.000; bootstrap: 79%)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-040718-362 (score: 1.000; bootstrap: 100%) ZDB-CDNA-040718-397 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Dictyostelium discoideum	DDB0189092 (score: 1.000; bootstrap: 78%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0036848 (score: 1.000; bootstrap: 89%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA15549-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000027161 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000311984 (score: 1.000; bootstrap: 67%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000003528 (score: 1.000; bootstrap: 65%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000005619 (score: 1.000; bootstrap: 73%)	From Inparanoid:20070104
Mus musculus	MGI:1913353 (score: 1.000; bootstrap: 66%)	From Inparanoid:20070104
Oryza gramene	Q53Q78 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000010257 (score: 1.000; bootstrap: 66%)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000021637 (score: 1.000; bootstrap: 66%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YKL151C (score: 1.000; bootstrap: 53%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPCC613 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000153020 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00025998001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000017993 (score: 1.000; bootstrap: 60%)	From Inparanoid:20070104
Shigella flexneri	YJEF	From SHIGELLACYC
E. coli O157	YJEF	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
Superfamily (EcoliWiki Page)	SUPERFAMILY:53613
Panther (EcoliWiki Page)	PTHR12592:SF0
Superfamily (EcoliWiki Page)	SUPERFAMILY:64153
Pfam (EcoliWiki Page)	PF01256 Carbohydrate kinase
Pfam (EcoliWiki Page)	PF03853 YjeF-related protein N-terminus
EcoCyc	EcoCyc:EG11758	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11758	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001694	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1708	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0013644	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 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).

yjeF: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 yjeF Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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