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Gene |

Product(s) |

Expression|

Evolution |

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Standard Name	ybaS
Gene Synonym(s)	ECK0479, b0485, JW0474^[1], JW0474
Product Desc.	predicted glutaminase^[2]^[3] Glutaminase^[4]
Product Synonyms(s)	predicted glutaminase^[1], YbaS^[2]^[1], B0485^[2]^[1] , ECK0479, JW0474, b0485
Function from GO	<GO_nr />
Knock-Out Phenotype
Regulation/Expression	transcription unit(s): ybaST^[2]
Regulation/Activity
Quick Links
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Notes

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Two glutaminases have been purified and biochemically characterized from E. coli B. ybaS might contribute to acid resistance (Brown, 2008).^[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	ybaS
Mnemonic	Systematic nomenclature
Synonyms	ECK0479, b0485, JW0474^[1], JW0474
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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	11.01 minutes	MG1655: 510865..511797 <gbrowseImage> name=NC_000913:510865..511797 source=MG1655 preset=GeneLocation </gbrowseImage>	EcoCyc GBrowse(MG1655)	FASTA Dump EcoCyc Sequence Dump
REL606		NC_012967: 483809..484741 <gbrowseImage> name=NC_012967:483809..484741 source=REL606 preset=GeneLocation </gbrowseImage>	GBrowse (REL606)	FASTA Dump
BW2952		NC_012759: 413624..414556 <gbrowseImage> name=NC_012759:413624..414556 source=BW2952 preset=GeneLocation </gbrowseImage>	GBrowse (BW2952)	FASTA Dump
W3110		W3110: 510865..511797 <gbrowseImage> name=NC_007779:510865..511797 source=W3110 preset=GeneLocation </gbrowseImage>	GBrowse(W3110)	FASTA Dump
DH10B		DH10B: 450196..451128 <gbrowseImage> name=NC_010473:450196..451128 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
ΔybaS (Keio:JW0474)	deletion	deletion	PMID:16738554	Shigen CGSC8626^[5]
ΔybaS768::kan			PMID:16738554	CGSC:103644
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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
JW0474	Plasmid clone	Shigen	PMID:16769691 Status:Clone OK Primer 1:GCCTTAGATGCAAACAAATTACA Primer 2:CCGCCCTTAAACACGTTATAGCC
4B10	Kohara Phage	Genobase	PMID:3038334
7C12	Kohara Phage	Genobase	PMID:3038334
gsk-3055::Tn10	Linked marker	CAG12154 = CGSC7341^[5]	est. P1 cotransduction: 72% ^[6] Synonyms:zbb-30-55::TnlO, zba-3055::Tn10
purK79::Tn10	Linked marker	CAG12171 = CGSC7342^[5]	est. P1 cotransduction: 17% ^[6] Synonyms:purE79::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:G6261	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13247	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002869	Escherichia coli str. K-12 substr. MG1655
NCBI (EcoliWiki Page)	GeneID:946187	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3036	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001688	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	YbaS
Synonyms	predicted glutaminase^[1], YbaS^[2]^[1], B0485^[2]^[1] , ECK0479, JW0474, b0485
Product description	predicted glutaminase^[2]^[3] Glutaminase^[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:0004359	glutaminase activity	GOA:hamap GO_REF:0000020	IEA: Inferred from Electronic Annotation	HAMAP:MF_00313	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004359	glutaminase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007043	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004359	glutaminase activity	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015868	F	Seeded from EcoCyc (v14.0)	complete
	GO:0004359	glutaminase activity	GOA:spec GO_REF:0000003	IEA: Inferred from Electronic Annotation	EC:3.5.1.2	F	Seeded from EcoCyc (v14.0)	complete
	GO:0006541	glutamine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR007043	P	Seeded from EcoCyc (v14.0)	complete
	GO:0006541	glutamine metabolic process	GOA:interpro GO_REF:0000002	IEA: Inferred from Electronic Annotation	InterPro:IPR015868	P	Seeded from EcoCyc (v14.0)	complete
	GO:0004359	glutaminase activity	PMID:18459799	IDA: Inferred from Direct Assay		F		complete
	GO:0045926	negative regulation of growth	PMID:18459799	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	rplS	PMID:19402753	LCMS(ID Probability):99.6
Protein	tig	PMID:19402753	LCMS(ID Probability):99.6
Protein	rraB	PMID:19402753	LCMS(ID Probability):99.6
Protein	dnaN	PMID:19402753	LCMS(ID Probability):99.6 MALDI(Z-score):26.703078
Protein	yccS	PMID:19402753	LCMS(ID Probability):99.6
Protein	yciU	PMID:19402753	LCMS(ID Probability):99.6
Protein	pspE	PMID:19402753	LCMS(ID Probability):99.6
Protein	arcA	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 MLDANKLQQA VDQAYTQFHS LNGGQNADYI PFLANVPGQL AAVAIVTCDG NVYSAGDSDY RFALESISKV CTLALALEDV GPQAVQDKIG ADPTGLPFNS VIALELHGGK PLSPLVNAGA IATTSLINAE NVEQRWQRIL HIQQQLAGEQ VALSDEVNQS EQTTNFHNRA IAWLLYSAGY LYCDAMEACD VYTRQCSTLL NTIELATLGA TLAAGGVNPL THKRVLQADN VPYILAEMMM EGLYGRSGDW AYRVGLPGKS GVGGGILAVV PGVMGIAAFS PPLDEDGNSV RGQKMVASVA KQLGYNVFKG
Length	310
Mol. Wt	32.902 kDa
pI	4.7 (calculated)
Extinction coefficient	34,380 - 35,005 (calc based on 12 Y, 3 W, and 5 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	24..308	PF04960 Glutaminase		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=ybaS 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:16128469	Escherichia coli str. K-12 substr. MG1655
NCBI (Protein) (EcoliWiki Page)	GeneID:946187	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001688	Escherichia coli str. K-12 substr. MG1655
UniProt (EcoliWiki Page)	UniProtKB/Swiss-Prot:P77454	Escherichia coli str. K-12 substr. MG1655
EcoCyc	EcoCyc:G6261	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13247	Escherichia coli str. K-12 substr. MG1655
NCBI (Gene) (EcoliWiki Page)	GeneID:946187	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002869	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3036	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	22.11+/-0.513	Molecules/cell	Medium: Temperature (°C): Doubling time (min): Growth Rate(min): * Growth phase: other: *		Single Molecule Fluorescence	PMID:20671182
mRNA	Ecoli K-12	0.163626609	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	13^a	molecules/cell/generation	Medium: MOPS Complete Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	PMID: 24766808
Protein	E. coli K-12 MG1655	317	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	0^a	molecules/cell/generation	Medium: MOPS Complete without Methionine Temperature (°C): 37 Doubling time (min): *Growth phase: OD: other:	Ribosome Profiling	Low confidence in the sequencing data set.	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)
ybaST
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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_000913:510845..510885 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:b0485 (EcoliWiki Page)	NCBI GEO profiles for ybaS
microarray	GenExpDB:b0485 (EcoliWiki Page)	Summary of data for ybaS 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 ybaS Expression

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

Database	Accession	Notes
EcoCyc	EcoCyc:G6261	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3036	Escherichia coli str. K-12 substr. MG1655
EcoliGenExpDB (EcoliWiki Page)	EcoliGenExpDB:b0485
EcoGene	EcoGene:EG13247	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002869	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001688	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
Bos taurus	ENSBTAP00000012231 (score: 1.000; bootstrap: 100%) ENSBTAP00000010348 (score: 0.418)	From Inparanoid:20070104
Caenorhabditis briggsae	WBGene00041999 (score: 1.000; bootstrap: 100%) WBGene00034134 (score: 0.350)	From Inparanoid:20070104
Caenorhabditis elegans	WBGene00007480 (score: 1.000; bootstrap: 100%) WBGene00008435 (score: 0.184) WBGene00009271 (score: 0.137)	From Inparanoid:20070104
Canis familiaris	ENSCAFP00000013987 (score: 1.000; bootstrap: 100%) ENSCAFP00000000194 (score: 0.757)	From Inparanoid:20070104
Danio rerio	ZDB-GENE-030616-550 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Gallus gallus	ENSGALP00000012199 (score: 1.000; bootstrap: 100%)	From Inparanoid:20070104
Homo sapiens	ENSP00000317379 (score: 1.000; bootstrap: 100%) ENSP00000310447 (score: 0.545)	From Inparanoid:20070104
Macaca mulatta	ENSMMUP00000007418 (score: 1.000; bootstrap: 100%) ENSMMUP00000001154 (score: 0.308)	From Inparanoid:20070104
Monodelphis domestica	ENSMODP00000014615 (score: 1.000; bootstrap: 100%) ENSMODP00000026445 (score: 0.546)	From Inparanoid:20070104
Mus musculus	MGI:95752 (score: 1.000; bootstrap: 100%) MGI:2143539 (score: 0.470)	From Inparanoid:20070104
Pan troglodytes	ENSPTRP00000021791 (score: 1.000; bootstrap: 100%) ENSPTRP00000008680 (score: 0.472)	From Inparanoid:20070104
Rattus norvegicus	ENSRNOP00000018818 (score: 1.000; bootstrap: 100%) ENSRNOP00000018737 (score: 0.696)	From Inparanoid:20070104
Takifugu rubripes	NEWSINFRUP00000176361 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000143899 (score: 1.000; bootstrap: 100%) NEWSINFRUP00000141445 (score: 0.144)	From Inparanoid:20070104
Tetraodon nigroviridis	GSTENP00031850001 (score: 1.000; bootstrap: 100%) GSTENP00023662001 (score: 1.000; bootstrap: 100%) GSTENP00003741001 (score: 0.145) GSTENP00029227001 (score: 0.074)	From Inparanoid:20070104
Shigella flexneri	YBAS	From SHIGELLACYC
E. coli O157	YBAS	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)	PF04960 Glutaminase
Superfamily (EcoliWiki Page)	SUPERFAMILY:56601
EcoCyc	EcoCyc:G6261	Escherichia coli str. K-12 substr. MG1655
EcoGene	EcoGene:EG13247	Escherichia coli str. K-12 substr. MG1655
RegulonDB	RegulonDB:ECK120002869	Escherichia coli str. K-12 substr. MG1655
EchoBASE	EchoBASE:EB3036	Escherichia coli str. K-12 substr. MG1655
ASAP	ASAP:ABE-0001688	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).

ybaS: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 ybaS Expression

Notes

Links

Evolution

Homologs in Other Organisms

Do-It-Yourself Web Tools

Notes

Families

Notes

Links

References

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