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On One Page

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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	yebC
Gene Synonym(s)	ECK1865, b1864, JW1853^[1], JW1853
Product Desc.	conserved protein^[2]^[3] Function unknown, expressed protein; non-essential gene^[4]
Product Synonyms(s)	conserved protein^[1], B1864^[2]^[1], YebC^[2]^[1] , ECK1865, JW1853, b1864
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): nudB-yebC-ruvC^[2], yebC-ruvC^[2]
Regulation/Activity
Quick Links
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Notes

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YeeN and YebC are paralogs. UPF0082.^[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	yebC
Mnemonic	Systematic nomenclature
Synonyms	ECK1865, b1864, JW1853^[1], JW1853
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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	41.93 minutes	MG1655: 1946175..1945435 <gbrowseImage> name=NC_000913:1945435..1946175 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 1926921..1926181 <gbrowseImage> name=NC_012967:1926181..1926921 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 1837494..1838234 <gbrowseImage> name=NC_012759:1837494..1838234 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 1949865..1949125 <gbrowseImage> name=NC_007779:1949125..1949865 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 2036746..2036006 <gbrowseImage> name=NC_010473:2036006..2036746 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	Comments
ΔyebC (Keio:JW1853)	deletion	deletion	PMID:16738554	Shigen CGSC9546^[5]
yebC::Tn5KAN-I-SceI (FB20480)	Insertion at nt 201 in Minus orientation		PMID:15262929	E. coli Genome Project:FB20480	contains pKD46
ΔyebC790::kan			PMID:16738554	CGSC:104410
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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
JW1853	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCGCAGGTCATAGTAAATGGGC Primer 2:CCGAGAGTCGCTGCGACCTCATC
20H4	Kohara Phage	Genobase	PMID:3038334
eda-51::Tn10	Linked marker	CAG18486 = CGSC7392^[5]	est. P1 cotransduction: 58% ^[6]
uvrC279::Tn10	Linked marker	CAG12156 = CGSC7394^[5]	est. P1 cotransduction: 14% ^[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:EG11137	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11137	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001121	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946379	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1127	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006219	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	YebC
Synonyms	conserved protein^[1], B1864^[2]^[1], YebC^[2]^[1] , ECK1865, JW1853, b1864
Product description	conserved protein^[2]^[3] Function unknown, expressed protein; non-essential gene^[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	argS	PMID:15690043	Experiment(s):EBI-893792
Protein	puuE	PMID:15690043	Experiment(s):EBI-893792
Protein	hdeD	PMID:15690043	Experiment(s):EBI-893792
Protein	sseA	PMID:15690043	Experiment(s):EBI-893792
Protein	stpA	PMID:16606699	Experiment(s):EBI-1141091
Protein	slyD	PMID:16606699	Experiment(s):EBI-1141091
Protein	nadE	PMID:16606699	Experiment(s):EBI-1141091
Protein	cybC	PMID:16606699	Experiment(s):EBI-1141091
Protein	rplQ	PMID:16606699	Experiment(s):EBI-1141091
Protein	purR	PMID:16606699	Experiment(s):EBI-1141091
Protein	rpsI	PMID:16606699	Experiment(s):EBI-1141091
Protein	def	PMID:16606699	Experiment(s):EBI-1141091
Protein	prs	PMID:16606699	Experiment(s):EBI-1141091
Protein	rpsN	PMID:16606699	Experiment(s):EBI-1141091
Protein	napC	PMID:16606699	Experiment(s):EBI-1141091
Protein	slyB	PMID:16606699	Experiment(s):EBI-1141091
Protein	argS	PMID:19402753	LCMS(ID Probability):99.6
Protein	tolB	PMID:19402753	MALDI(Z-score):37.565951
Protein	znuA	PMID:19402753	LCMS(ID Probability):99.4 MALDI(Z-score):37.279597
Protein	puuE	PMID:19402753	LCMS(ID Probability):99.6
Protein	hdeD	PMID:19402753	LCMS(ID Probability):99.6
Protein	sseA	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 MAGHSKWANT RHRKAAQDAK RGKIFTKIIR ELVTAAKLGG GDPDANPRLR AAVDKALSNN MTRDTLNRAI ARGVGGDDDA NMETIIYEGY GPGGTAIMIE CLSDNRNRTV AEVRHAFSKC GGNLGTDGSV AYLFSKKGVI SFEKGDEDTI MEAALEAGAE DVVTYDDGAI DVYTAWEEMG KVRDALEAAG LKADSAEVSM IPSTKADMDA ETAPKLMRLI DMLEDCDDVQ EVYHNGEISD EVAATL
Length	246
Mol. Wt	26.422 kDa
pI	4.6 (calculated)
Extinction coefficient	19,940 - 20,315 (calc based on 6 Y, 2 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	Notes	References
Domain	5..237	PF01709 Domain of unknown function DUF28		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=yebC 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:16129817	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946379	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006219	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P0A8A0	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:EG11137	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11137	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946379	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001121	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1127	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	E. coli K-12 MC4100	8.19E+03	molecules/cell	Medium: median data from rich and minimal media Temperature (°C): 37 Doubling time (min): Growth Rate(min): Growth phase: other:	emPAI		PMID:18304323
Protein	Ecoli K-12	162.088+/-0.836	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.34454+/-0.0453	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		by FISH	PMID:20671182
mRNA	Ecoli K-12	0.232432432	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	13702	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	2970	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	9115	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)
nudB-yebC-ruvC
yebC-ruvC
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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_000913:1946155..1946195 source=MG1655 flip=1 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:b1864 (EcoliWiki Page)	NCBI GEO profiles for yebC
microarray	GenExpDB:b1864 (EcoliWiki Page)	Summary of data for yebC 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 yebC Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:EG11137	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1127	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b1864
EcoGene	EcoGene:EG11137	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001121	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006219	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	ENSANGP00000008570 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Arabidopsis thaliana	AT2G25830 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Bos taurus	ENSBTAP00000013031 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00035860 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00021757 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000019068 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Ciona intestinalis	ENSCINP00000019427 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila melanogaster	FBgn0032205 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Drosophila pseudoobscura	GA18554-PA (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000258975 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000019115 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000012507 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Mus musculus	MGI:1917457 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Oryza gramene	Q6F2Z2 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000016156 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Saccharomyces cerevisiae	YGR021W (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Schizosaccharomyces pombe	SPBC8D22c (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000162175 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00035040001 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Xenopus tropicalis	ENSXETP00000007057 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Shigella flexneri	YEBC	From SHIGELLACYC
E. coli O157	YEBC	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)	PF01709 Domain of unknown function DUF28
Superfamily (EcoliWiki Page)	SUPERFAMILY:75625
EcoCyc	EcoCyc:EG11137	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG11137	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120001121	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB1127	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0006219	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 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).

yebC: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 yebC Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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